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Sample records for induces loop structures

  1. Involvement of the V1/V2 variable loop structure in the exposure of human immunodeficiency virus type 1 gp120 epitopes induced by receptor binding.

    PubMed Central

    Wyatt, R; Moore, J; Accola, M; Desjardin, E; Robinson, J; Sodroski, J

    1995-01-01

    The binding of human immunodeficiency virus type 1 (HIV-1) to the cellular receptor CD4 has been suggested to induce conformational changes in the viral envelope glycoproteins that promote virus entry. Conserved, discontinuous epitopes on the HIV-1 gp120 glycoprotein recognized by the 17b, 48d, and A32 antibodies are preferentially exposed upon the binding of soluble CD4 (sCD4). The binding of the 17b and 48d antibodies to the gp120 glycoprotein can also be enhanced by the binding of the A32 antibody. Here we constructed HIV-1 gp120 mutants in which the variable segments of the V1/V2 and V3 structures were deleted, individually or in combination, while the 17b, 48d, and A32 epitopes were retained. The effects of the variable loop deletions on the function of the HIV-1 envelope glycoproteins and on the exposure of epitopes induced by sCD4 or A32 binding to the monomeric gp120 glycoprotein were examined. The variable-loop-deleted envelope glycoproteins were able to mediate virus entry, albeit at lower efficiencies than those of the wild-type glycoproteins. Thus, the V1/V2 and V3 variable sequences contribute to the efficiency of HIV-1 entry but are not absolutely required for the process. Neither the V1/V2 nor V3 loops were necessary for the increase in exposure of the 17b/48d epitopes induced by binding of the A32 monoclonal antibody. By contrast, induction of the 17b, 48d, and A32 epitopes by sCD4 binding apparently involves a movement of the V1/V2 loops, which in the absence of CD4 partially mask these epitopes on the native gp120 monomer. The results obtained with a mutant glycoprotein containing a deletion of the V1 loop alone indicated that the contribution of the V2 loop to these phenomena was more significant than that of the V1 sequences. These results suggest that the V1/V2 loops, which have been previously implicated in CD4-modulated, postattachment steps in HIV-1 entry, contribute to CD4-induced gp120 conformational changes detected by the 17b, 48d, and A

  2. Structure of stem-loop IV of Tetrahymena telomerase RNA

    PubMed Central

    Chen, Yu; Fender, Jessica; Legassie, Jason D; Jarstfer, Michael B; Bryan, Tracy M; Varani, Gabriele

    2006-01-01

    Conserved domains within the RNA component of telomerase provide the template for reverse transcription, recruit protein components to the holoenzyme and are required for enzymatic activity. Among the functionally essential domains in ciliate telomerase RNA is stem-loop IV, which strongly stimulates telomerase activity and processivity even when provided in trans. The NMR structure of Tetrahymena thermophila stem-loop IV shows a highly structured distal stem-loop linked to a conformationally flexible template-proximal region by a bulge that severely kinks the entire RNA. Through extensive structure–function studies, we identify residues that contribute to both these structural features and to enzymatic activity, with no apparent effect on the binding of TERT protein. We propose that the bending induced by the GA bulge and the flexibility of the template-proximal region allow positioning of the prestructured apical loop during the catalytic cycle. PMID:16778765

  3. Pressure structure of solar coronal loops

    NASA Technical Reports Server (NTRS)

    Krishan, V.

    1987-01-01

    The steady state pressure structure of a coronal loop is discussed in terms of the MHD global invariants of an incompressible plasma. The steady state is represented by the superposition of two Chandrasekhar-Kendall functions corresponding to (n=m=0) and (n=m=1) modes. The relative contribution of the two modes (epsilon) is found to depend on the surface pressure of the coronal loop which is also the pressure of the external medium. The mixed mode state does not exist for high values of the external pressure because epsilon becomes complex.

  4. Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

    PubMed Central

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence–structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. PMID:19923230

  5. Magnetic fine structure of solar coronal loops

    NASA Technical Reports Server (NTRS)

    Van Ballegooijen, A. A.

    1988-01-01

    A numerical simulation of the effect of a random photospheric flow on the magnetic structure of a coronal loop is presented. An initially uniform field embedded in a perfectly conducting plasma is assumed, extending between two flat parallel plates representing the solar photosphere at both ends of the loop. The field is perturbed by a sequence of randomly phased, sinusoidal flow patterns applied at one of the boundary plates, and the corresponding sequence of force-free fields is determined. It is found that the electric currents generated by these flows develop a fine structure on a scale significantly smaller than the wavelength of the velocity patterns. This suggests that magnetic energy is transferred to smaller scale via a cascade process.

  6. Fast loop modeling for protein structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  7. The Fundamental Structure of Coronal Loops

    NASA Technical Reports Server (NTRS)

    Winebarger, Amy; Warren, Harry; Cirtain, Jonathan; Kobayashi, Ken; Korreck, Kelly; Golub, Leon; Kuzin, Sergey; Walsh, Robert; DePontieu, Bart; Title, Alan; Weber, Mark

    2012-01-01

    During the past ten years, solar physicists have attempted to infer the coronal heating mechanism by comparing observations of coronal loops with hydrodynamic model predictions. These comparisons often used the addition of sub ]resolution strands to explain the observed loop properties. On July 11, 2012, the High Resolution Coronal Imager (Hi ]C) was launched on a sounding rocket. This instrument obtained images of the solar corona was 0.2 ]0.3'' resolution in a narrowband EUV filter centered around 193 Angstroms. In this talk, we will compare these high resolution images to simultaneous density measurements obtained with the Extreme Ultraviolet Imaging Spectrograph (EIS) on Hinode to determine whether the structures observed with Hi ]C are resolved.

  8. Early structure formation from cosmic string loops

    SciTech Connect

    Shlaer, Benjamin; Vilenkin, Alexander; Loeb, Abraham E-mail: vilenkin@cosmos.phy.tufts.edu

    2012-05-01

    We examine the effects of cosmic strings on structure formation and on the ionization history of the universe. While Gaussian perturbations from inflation are known to provide the dominant contribution to the large scale structure of the universe, density perturbations due to strings are highly non-Gaussian and can produce nonlinear structures at very early times. This could lead to early star formation and reionization of the universe. We improve on earlier studies of these effects by accounting for high loop velocities and for the filamentary shape of the resulting halos. We find that for string energy scales Gμ∼>10{sup −7}, the effect of strings on the CMB temperature and polarization power spectra can be significant and is likely to be detectable by the Planck satellite. We mention shortcomings of the standard cosmological model of galaxy formation which may be remedied with the addition of cosmic strings, and comment on other possible observational implications of early structure formation by strings.

  9. An Antibody Loop Replacement Design Feasibility Study and a Loop-Swapped Dimer Structure

    SciTech Connect

    Clark, L.; Boriack-Sjodin, P; Day, E; Eldredge, J; Fitch, C; Jarpe, M; Miller, S; Li, Y; Simon, K; van Vlijmen, H

    2009-01-01

    A design approach was taken to investigate the feasibility of replacing single complementarity determining region (CDR) antibody loops. This approach may complement simpler mutation-based strategies for rational antibody design by expanding conformation space. Enormous crystal structure diversity is available, making CDR loops logical targets for structure-based design. A detailed analysis for the L1 loop shows that each loop length takes a distinct conformation, thereby allowing control on a length scale beyond that accessible to simple mutations. The L1 loop in the anti-VLA1 antibody was replaced with the L2 loop residues longer in an attempt to add an additional hydrogen bond and fill space on the antibody-antigen interface. The designs expressed well, but failed to improve affinity. In an effort to learn more, one design was crystallized and data were collected at 1.9 {angstrom} resolution. The designed L1 loop takes the qualitatively desired conformation; confirming that loop replacement by design is feasible. The crystal structure also shows that the outermost loop (residues Leu51-Ser68) is domain swapped with another monomer. Tryptophan fluorescence measurements were used to monitor unfolding as a function of temperature and indicate that the loop involved in domain swapping does not unfold below 60C. The domain-swapping is not directly responsible for the affinity loss, but is likely a side-effect of the structural instability which may contribute to affinity loss. A second round of design was successful in eliminating the dimerization through mutation of a residue (Leu51Ser) at the joint of the domain-swapped loop.

  10. Structure Prediction of RNA Loops with a Probabilistic Approach

    PubMed Central

    Li, Jun; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

    2016-01-01

    The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction. PMID:27494763

  11. Automated event generation for loop-induced processes

    DOE PAGESBeta

    Hirschi, Valentin; Mattelaer, Olivier

    2015-10-22

    We present the first fully automated implementation of cross-section computation and event generation for loop-induced processes. This work is integrated in the MadGraph5_aMC@NLO framework. We describe the optimisations implemented at the level of the matrix element evaluation, phase space integration and event generation allowing for the simulation of large multiplicity loop-induced processes. Along with some selected differential observables, we illustrate our results with a table showing inclusive cross-sections for all loop-induced hadronic scattering processes with up to three final states in the SM as well as for some relevant 2 → 4 processes. Furthermore, many of these are computed heremore » for the first time.« less

  12. Automated event generation for loop-induced processes

    NASA Astrophysics Data System (ADS)

    Hirschi, Valentin; Mattelaer, Olivier

    2015-10-01

    We present the first fully automated implementation of cross-section computation and event generation for loop-induced processes. This work is integrated in the M adG raph5_ aMC@NLO framework. We describe the optimisations implemented at the level of the matrix element evaluation, phase space integration and event generation allowing for the simulation of large multiplicity loop-induced processes. Along with some selected differential observables, we illustrate our results with a table showing inclusive cross-sections for all loop-induced hadronic scattering processes with up to three final states in the SM as well as for some relevant 2 → 4 processes. Many of these are computed here for the first time.

  13. Automated event generation for loop-induced processes

    SciTech Connect

    Hirschi, Valentin; Mattelaer, Olivier

    2015-10-22

    We present the first fully automated implementation of cross-section computation and event generation for loop-induced processes. This work is integrated in the MadGraph5_aMC@NLO framework. We describe the optimisations implemented at the level of the matrix element evaluation, phase space integration and event generation allowing for the simulation of large multiplicity loop-induced processes. Along with some selected differential observables, we illustrate our results with a table showing inclusive cross-sections for all loop-induced hadronic scattering processes with up to three final states in the SM as well as for some relevant 2 → 4 processes. Furthermore, many of these are computed here for the first time.

  14. Coarse-Grained Prediction of RNA Loop Structures

    PubMed Central

    Liu, Liang; Chen, Shi-Jie

    2012-01-01

    One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed “Vfold” model (a coarse-grained RNA folding model) provides an effective method to generate the complete ensemble of coarse-grained RNA loop and junction conformations. However, due to the lack of sequence-dependent scoring parameters, the method is unable to identify the native and near-native structures from the sequence. In this study, using a previously developed iterative method for extracting the knowledge-based potential parameters from the known structures, we derive a set of dinucleotide-based statistical potentials for RNA loops and junctions. A unique advantage of the approach is its ability to go beyond the the (known) native structures by accounting for the full free energy landscape, including all the nonnative folds. The benchmark tests indicate that for given loop/junction sequences, the statistical potentials enable successful predictions for the coarse-grained 3D structures from the complete conformational ensemble generated by the Vfold model. The predicted coarse-grained structures can provide useful initial folds for further detailed structural refinement. PMID:23144887

  15. Control-structure interaction in precision pointing servo loops

    NASA Technical Reports Server (NTRS)

    Spanos, John T.

    1989-01-01

    The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

  16. Observation of Nonlinear Looped Band Structure of Bose-Einstein condensates in an optical lattice

    NASA Astrophysics Data System (ADS)

    Goldschmidt, Elizabeth; Koller, Silvio; Brown, Roger; Wyllie, Robert; Wilson, Ryan; Porto, Trey

    2016-05-01

    We study experimentally the stability of excited, interacting states of bosons in a double-well optical lattice in regimes where the nonlinear interactions are expected to induce ``swallow-tail'' looped band structure. By carefully preparing different initial coherent states and observing their subsequent decay, we observe distinct decay rates, which provide direct evidence for multi-valued band structure. The double well lattice both stabilizes the looped band structure and allows for dynamic preparation of different initial states, including states within the loop structure. We confirm our state preparation procedure with dynamic Gross-Pitaevskii calculations. The excited loop states are found to be more stable than dynamically unstable ground states, but decay faster than expected based on a mean-field stability calculation, indicating the importance of correlations beyond a mean-field description. Now at Georgia Tech Research Institute.

  17. FINE STRUCTURES AND OVERLYING LOOPS OF CONFINED SOLAR FLARES

    SciTech Connect

    Yang, Shuhong; Zhang, Jun; Xiang, Yongyuan

    2014-10-01

    Using the Hα observations from the New Vacuum Solar Telescope at the Fuxian Solar Observatory, we focus on the fine structures of three confined flares and the issue why all the three flares are confined instead of eruptive. All the three confined flares take place successively at the same location and have similar morphologies, so can be termed homologous confined flares. In the simultaneous images obtained by the Solar Dynamics Observatory, many large-scale coronal loops above the confined flares are clearly observed in multi-wavelengths. At the pre-flare stage, two dipoles emerge near the negative sunspot, and the dipolar patches are connected by small loops appearing as arch-shaped Hα fibrils. There exists a reconnection between the small loops, and thus the Hα fibrils change their configuration. The reconnection also occurs between a set of emerging Hα fibrils and a set of pre-existing large loops, which are rooted in the negative sunspot, a nearby positive patch, and some remote positive faculae, forming a typical three-legged structure. During the flare processes, the overlying loops, some of which are tracked by activated dark materials, do not break out. These direct observations may illustrate the physical mechanism of confined flares, i.e., magnetic reconnection between the emerging loops and the pre-existing loops triggers flares and the overlying loops prevent the flares from being eruptive.

  18. Saturating representation of loop conformational fragments in structure databanks

    PubMed Central

    Fernandez-Fuentes, Narcis; Fiser, András

    2006-01-01

    Background Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments in structure databanks. Results We studied the representation of protein loop fragments up to 14 residues in length. All possible query fragments found in sequence databases (Sequence Space) were clustered and cross referenced with available structural fragments in Protein Data Bank (Structure Space). We found that the expansion of PDB in the last few years resulted in a dense coverage of loop conformational fragments. For each loops of length 8 in the current Sequence Space there is at least one loop in Structure Space with 50% or higher sequence identity. By correlating sequence and structure clusters of loops we found that a 50% sequence identity generally guarantees structural similarity. These percentages of coverage at 50% sequence cutoff drop to 96, 94, 68, 53, 33 and 13% for loops of length 9, 10, 11, 12, 13, and 14, respectively. There is not a single loop in the current Sequence Space at any length up to 14 residues that is not matched with a conformational segment that shares at least 20% sequence identity. This minimum observed identity is 40% for loops of 12 residues or shorter and is as high as 50% for 10 residue or shorter loops. We also assessed the impact of rapidly growing sequence databanks on the estimated number of new loop conformations and found that while the number of sequentially unique sequence segments increased about six folds during the last five years there are almost no unique conformational segments among these up to 12 residues long fragments. Conclusion The results suggest that fragment based prediction approaches are not limited any more by the completeness of fragments in databanks but rather by the effective

  19. Asymmetric structure of five and six membered DNA hairpin loops

    NASA Technical Reports Server (NTRS)

    Baumann, U.; Chang, S.

    1995-01-01

    The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

  20. ArchPRED: a template based loop structure prediction server.

    PubMed

    Fernandez-Fuentes, Narcis; Zhai, Jun; Fiser, András

    2006-07-01

    ArchPRED server (http://www.fiserlab.org/servers/archpred) implements a novel fragment-search based method for predicting loop conformations. The inputs to the server are the atomic coordinates of the query protein and the position of the loop. The algorithm selects candidate loop fragments from a regularly updated loop library (Search Space) by matching the length, the types of bracing secondary structures of the query and by satisfying the geometrical restraints imposed by the stem residues. Subsequently, candidate loops are inserted in the query protein framework where their side chains are rebuilt and their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed [/psi] main chain dihedral angle propensities. The final loop conformation is built in the protein structure and annealed in the environment using conjugate gradient minimization. The prediction method was benchmarked on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it was possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head to head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method. PMID:16844985

  1. Structural study of elements of Tetrahymena telomerase RNA stem–loop IV domain important for function

    PubMed Central

    Richards, Rebecca J.; Wu, Haihong; Trantirek, Lukas; O'Connor, Catherine M.; Collins, Kathleen; Feigon, Juli

    2006-01-01

    Tetrahymena telomerase RNA (TER) contains several regions in addition to the template that are important for function. Central among these is the stem–loop IV domain, which is involved in both catalysis and RNP assembly, and includes binding sites for both the holoenzyme assembly protein p65 and telomerase reverse transcriptase (TERT). Stem–loop IV contains two regions with high evolutionary sequence conservation: a central GA bulge between helices, and a terminal loop. We solved the solution structure of loop IV and modeled the structure of the helical region containing the GA bulge, using NMR and residual dipolar couplings. The central GA bulge with flanking C–G base pairs induces a ∼50° semi-rigid bend in the helix. Loop IV is highly structured, and contains a conserved C–U base pair at the top of the helical stem. Analysis of new and previous biochemical data in light of the structure provides a rationale for some of the sequence conservation in this region of TER. The results suggest that during holoenzyme assembly the protein p65 recognizes a bend in stem IV, and this binding to central stem IV helps to position the structured loop IV for interaction with TERT and other region(s) of TER. PMID:16809815

  2. A simple algorithm for the generation of efficient loop structures

    SciTech Connect

    Cosnard, M.; Loi, M.

    1996-06-01

    Generating code to enumerate the integer points of a polyhedron is a key problem of the parallelizing compiler technology. For efficiency reasons we want to obtain loop bounds of the generated code that are as simple as possible and we would like to avoid executing iterations of outer loops for which no iterations of inner loops are executed. This paper describes a simple algorithm to build an adequate representation of the domain to enumerate, the Hierarchical Domain Descriptor (HDD). Starting from the HDD, generating such efficient loop structures is straightforward. In some particular but frequently occurring cases the HDD may also be used to count in a symbolic way the number of integer points contained in the domain.

  3. On the structure of solar and stellar coronae - Loops and loop heat transport

    NASA Technical Reports Server (NTRS)

    Litwin, Christof; Rosner, Robert

    1993-01-01

    We discuss the principal constraints on mechanisms for structuring and heating the outer atmospheres - the coronae - of stars. We argue that the essential cause of highly localized heating in the coronae of stars like the sun is the spatially intermittent nature of stellar surface magnetic fields, and that the spatial scale of the resulting coronal structures is related to the spatial structure of the photospheric fields. We show that significant constraints on coronal heating mechanisms derive from the observed variations in coronal emission, and, in addition, show that the observed structuring perpendicular to coronal magnetic fields imposes severe constraints on mechanisms for heat dispersal in the low-beta atmosphere. In particular, we find that most of commonly considered mechanisms for heat dispersal, such as anomalous diffusion due to plasma turbulence or magnetic field line stochasticity, are much too slow to account for the observed rapid heating of coronal loops. The most plausible mechanism appears to be reconnection at the interface between two adjacent coronal flux bundles. Based on a model invoking hyperresistivity, we show that such a mechanism naturally leads to dominance of isolated single bright coronal loops and to bright coronal plasma structures whose spatial scale transverse to the local magnetic field is comparable to observed dimensions of coronal X-ray loops.

  4. LINE-OF-SIGHT SHELL STRUCTURE OF THE CYGNUS LOOP

    SciTech Connect

    Uchida, Hiroyuki; Tsunemi, Hiroshi; Katsuda, Satoru; Kimura, Masashi; Kosugi, Hiroko; Takahashi, Hiroaki

    2009-11-10

    We conducted a comprehensive study on the shell structure of the Cygnus Loop using 41 observation data obtained by the Suzaku and the XMM-Newton satellites. To investigate the detailed plasma structure of the Cygnus Loop, we divided our fields of view into 1042 box regions. From the spectral analysis, the spectra obtained from the limb of the Loop are well fitted by the single-component non-equilibrium ionization plasma model. On the other hand, the spectra obtained from the inner regions are well fitted by the two-component model. As a result, we confirmed that the low-temperature and high-temperature components originated from the surrounding interstellar matter (ISM) and the ejecta of the Loop, respectively. From the best-fit results, we showed a flux distribution of the ISM component. The distribution clearly shows the limb-brightening structure, and we found out some low-flux regions. Among them, the south blowout region has the lowest flux. We also found other large low-flux regions at slightly west and northeast from the center. We estimated the former thin shell region to be approx1.{sup 0}3 in diameter and concluded that there exists a blowout along the line of sight in addition to the south blowout. We also calculated the emission measure distribution of the ISM component and showed that the Cygnus Loop is far from the result obtained by a simple Sedov evolution model. From the results, we support that the Cygnus Loop originated from a cavity explosion. The emission measure distribution also suggests that the cavity-wall density is higher in the northeast than that in the southwest. These results suggest that the thickness of the cavity wall surrounding the Cygnus Loop is not uniform.

  5. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.

    PubMed

    Fernandez-Fuentes, Narcis; Querol, Enrique; Aviles, Francesc X; Sternberg, Michael J E; Oliva, Baldomero

    2005-09-01

    In protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about phi-psi angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI-BLAST. A jack-knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X-ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI-PRED (Jones, J Mol Biol 1999;292:195-202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations. PMID:16021623

  6. Electrical resistance of complex two-dimensional structures of loops

    NASA Astrophysics Data System (ADS)

    Gomes, M. A. F.; Hora, R. R.; Brito, V. P.

    2011-06-01

    This work presents a study of the dc electrical resistance of a recently discovered hierarchical two-dimensional system which has a complex topology consisting of a distribution of disordered macroscopic loops with no characteristic size and a distribution of several types of contacts between loops. In addition to its intrinsic interest in the important context of low-dimensional systems and crumpled systems, the structures under study are of relevance in a number of areas including soft condensed matter and packing of DNA in viral capsids. In the particular case discussed here, the loops are made of layers of graphite with a height of tens of nanometers deposited on a substrate of cellulose. Experiments with these systems indicate an anomalous electrical resistance of sub-diffusive type. The results reported here are explained with scaling arguments and computer simulation. A comparison with the dc electrical properties of percolation clusters is made, and some other experimental issues as future prospects are commented.

  7. Structural studies on an internal loop from a hairpin ribozyme

    SciTech Connect

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr.

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  8. Collider study on the loop-induced dark matter mediation

    NASA Astrophysics Data System (ADS)

    Tsai, Yuhsin

    2016-06-01

    Collider experiments are one of the most promising ways to constrain Dark Matter (DM) interactions. For DM couplings involving light mediators, especially for the loop-mediated interactions, a meaningful interpretation of the results requires to go beyond effective field theory. In this note we discuss the study of the magnetic dipole interacting DM, focusing on a model with anarchic dark flavor structure. By including the momentum-dependent form factors that mediate the coupling - given by the Dark Penguin - in collider processes, we study bounds from monophoton, diphoton, and non-pointing photon searches at the LHC. We also compare our results to constraints from the direct detection experiments.

  9. SELF-ORGANIZED BRAIDING AND THE STRUCTURE OF CORONAL LOOPS

    SciTech Connect

    Berger, Mitchell A.; Asgari-Targhi, Mahboubeh E-mail: m.asgari@ucl.ac.u

    2009-11-01

    The Parker model for heating of the solar corona involves reconnection of braided magnetic flux elements. Much of this braiding is thought to occur at as yet unresolved scales, for example, braiding of threads within an extreme-ultraviolet or X-ray loop. However, some braiding may be still visible at scales accessible to TRACE or Hinode. We suggest that attempts to estimate the amount of braiding at these scales must take into account the degree of coherence of the braid structure. In this paper, we examine the effect of reconnection on the structure of a braided magnetic field. We demonstrate that simple models of braided magnetic fields which balance the input of topological structure with reconnection evolve to a self-organized critical state. An initially random braid can become highly ordered, with coherence lengths obeying power-law distributions. The energy released during reconnection also obeys a power law. Our model gives more frequent (but smaller) energy releases nearer to the ends of a coronal loop.

  10. An Id-related helix-loop-helix protein encoded by a growth factor-inducible gene.

    PubMed Central

    Christy, B A; Sanders, L K; Lau, L F; Copeland, N G; Jenkins, N A; Nathans, D

    1991-01-01

    An mRNA encoding a helix-loop-helix protein that we have named HLH462 is induced in mouse 3T3 cells as part of the immediate early transcriptional response to growth factors and other signaling agents. The RNA is present in a number of mouse tissues and in the developing mouse fetus. The HLH462 gene has been mapped by interspecific backcross analysis to the distal region of mouse chromosome 4. In its helix-loop-helix region HLH462 is closely related to the Id protein and the Drosophila emc protein. Like Id, HLH462 lacks a basic region required for DNA binding, and it inhibits the DNA-binding activities of other helix-loop-helix proteins. On the basis of its structural and functional similarity to Id, we suggest that HLH462 may inhibit the activities of helix-loop-helix transcription factors during the cellular growth response and during development. Images PMID:2000388

  11. Porous Foam Based Wick Structures for Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    Silk, Eric A.

    2012-01-01

    As part of an effort to identify cost efficient fabrication techniques for Loop Heat Pipe (LHP) construction, NASA Goddard Space Flight Center's Cryogenics and Fluids Branch collaborated with the U.S. Naval Academy s Aerospace Engineering Department in Spring 2012 to investigate the viability of carbon foam as a wick material within LHPs. The carbon foam was manufactured by ERG Aerospace and machined to geometric specifications at the U.S. Naval Academy s Materials, Mechanics and Structures Machine Shop. NASA GSFC s Fractal Loop Heat Pipe (developed under SBIR contract #NAS5-02112) was used as the validation LHP platform. In a horizontal orientation, the FLHP system demonstrated a heat flux of 75 Watts per square centimeter with deionized water as the working fluid. Also, no failed start-ups occurred during the 6 week performance testing period. The success of this study validated that foam can be used as a wick structure. Furthermore, given the COTS status of foam materials this study is one more step towards development of a low cost LHP.

  12. Solution structure of a five-adenine bulge loop within a DNA duplex.

    PubMed

    Dornberger, U; Hillisch, A; Gollmick, F A; Fritzsche, H; Diekmann, S

    1999-09-28

    The three-dimensional solution structure of a DNA molecule of the sequence 5'-d(GCATCGAAAAAGCTACG)-3' paired with 5'-d(CGTAGCCGATGC)-3' containing a five-adenine bulge loop (dA(5)-bulge) between two double helical stems was determined by 2D (1)H and (31)P NMR, infrared, and Raman spectroscopy. The DNA in both stems adopt a classical B-form double helical structure with Watson-Crick base pairing and C2'-endo sugar conformation. In addition, the two dG/dC base pairs framing the dA(5)-bulge loop are formed and are stable at least up to 30 degrees C. The five adenine bases of the bulge loop are localized at intrahelical positions within the double helical stems. Stacking on the double helical stem is continued for the first four 5'-adenines in the bulge loop. The total rise (the height) of these four stacked adenines roughly equals the diameter of the double helical stem. The stacking interactions are broken between the last of these four 5'-adenines and the fifth loop adenine at the 3'-end. This 3'-adenine partially stacks on the other stem. The angle between the base planes of the two nonstacking adenines (A10 and A11) in the bulge loop reflects the kinking angle of the global DNA structure. The neighboring cytosines opposite the dA(5)-bulge (being parts of the bulge flanking base pairs) do not stack on one another. This disruption of stacking is characterized by a partial shearing of these bases, such that certain sequential NOEs for this base step are preserved. In the base step opposite the loop, an extraordinary hydrogen bond is observed between the phosphate backbone of the 5'-dC and the amino proton of the 3'-dC in about two-thirds of the conformers. This hydrogen bond probably contributes to stabilizing the global DNA structure. The dA(5)-bulge induces a local kink into the DNA molecule of about 73 degrees (+/-11 degrees ). This kinking angle and the mutual orientation of the two double helical stems agree well with results from fluorescence resonance energy

  13. Plasmon induced transparency in loop-stub resonator-coupled waveguide systems

    NASA Astrophysics Data System (ADS)

    Ye, Jiulin; Wang, Faqiang; Liang, Ruisheng; Wei, Zhongchao; Meng, Hongyun; Zhong, Jiewen; Jiang, Lihua

    2016-07-01

    We firstly investigate plasmon induced transparency (PIT) effect in a metal-dielectric-metal (MDM) waveguide coupled to a single loop stub resonator by finite difference time domain method (FDTD). Compared with previous PIT sup based on MDM waveguide, PIT phenomena can be realized in a single plasmonic composite nanocavity without employment of additional optical elements. Plasmon induced transparency windows can be controlled by adjusting the geometrical parameters of the vertical branches or the horizontal branch in the plasmonic structure. The red-shift of PIT peak is almost linearly proportional to the refractive index of the horizontal branch. This plasmonic system takes the advantages of easy fabrication and compactness. The results may pave a way for the dynamic control of light in highly integrated optical circuits, which can realize ultrafast switching, light storage and nanosensor devices.

  14. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  15. Effect of self-induced magnetic force in a coronal loop transient

    NASA Technical Reports Server (NTRS)

    Yeh, T.; Dryer, M.

    1981-01-01

    The distribution of the self-induced magnetic force in a section of a model coronal loop is examined and it is found that an axial current produces a pointwise magnetic force in the direction toward the axis of the loop. The direction of the pointwise magnetic force indicates that the effect of this force, acting alone, is to cause a contraction of the cross section of the magnetic loop toward the axis, but not the translation motion of the loop as a whole. It is concluded that forces other than the self-induced magnetic force, such as thermal force of pressure gradient or extra-induced magnetic force of magnetic buoyancy, must be involved in the acceleration mechanisms for the heliocentrifugal motion of coronal transients.

  16. Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

    SciTech Connect

    Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

    2012-03-27

    RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

  17. Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

    PubMed

    Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

    2011-11-15

    RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

  18. The structure, stability and flaring of solar coronal loops

    NASA Technical Reports Server (NTRS)

    Van Hoven, G.

    1982-01-01

    A review is given of recent progress in the theory of the magnetohydrodynamic behavior of coronal loops, beginning with a brief characterization of thy observations. The equilibrium magnetic field is described, along with the consequences of the empirical requirement for short-term, or infinite-conductivity, stability which is shown to be dominated by the end-effect influence of thy quasi-rigid photosphere. A new loop-flare model is then developed, which takes account of the finite loop length. The primary resistive-sausage-mode instability exhibits the necessary threshold behavior, and produces a number of spatially and energetically distinct flare-release manifestations.

  19. A supersecondary structure library and search algorithm for modeling loops in protein structures

    PubMed Central

    Fernandez-Fuentes, Narcis; Oliva, Baldomero; Fiser, András

    2006-01-01

    We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105 950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed ϕ/ψ main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 Å of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a ∼5:1 ratio an

  20. A supersecondary structure library and search algorithm for modeling loops in protein structures.

    PubMed

    Fernandez-Fuentes, Narcis; Oliva, Baldomero; Fiser, András

    2006-01-01

    We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5

  1. Iterative structure within the five-particle two-loop amplitude

    SciTech Connect

    Cachazo, Freddy; Spradlin, Marcus; Volovich, Anastasia

    2006-08-15

    We find an unexpected iterative structure within the two-loop five-gluon amplitude in N=4 supersymmetric Yang-Mills theory. Specifically, we show that a subset of diagrams contributing to the full amplitude, including a two-loop pentagon-box integral with nontrivial dependence on five kinematical variables, satisfies an iterative relation in terms of one-loop scalar box diagrams. The implications of this result for the possible iterative structure of the full two-loop amplitude are discussed.

  2. A modular perspective of protein structures: application to fragment based loop modeling.

    PubMed

    Fernandez-Fuentes, Narcis; Fiser, Andras

    2013-01-01

    Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations we describe our loop conformation modeling algorithm, ArchPred that takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties the method narrows down possible template conformations in other, often not homologous structures, by identifying the most likely supersecondary structure environment that cradles the loop. Beyond identifying the correct starting supersecondary structure geometry, it takes into account information of fit of anchor residues, sterical clashes, match of predicted and observed dihedral angle preferences, and local sequence signal.

  3. Systematic U(1 ) B - L extensions of loop-induced neutrino mass models with dark matter

    NASA Astrophysics Data System (ADS)

    Ho, Shu-Yu; Toma, Takashi; Tsumura, Koji

    2016-08-01

    We study the gauged U(1 ) B - L extensions of the models for neutrino masses and dark matter. In this class of models, tiny neutrino masses are radiatively induced through the loop diagrams, while the origin of the dark matter stability is guaranteed by the remnant of the gauge symmetry. Depending on how the lepton number conservation is violated, these models are systematically classified. We present complete lists for the one-loop Z2 and the two-loop Z3 radiative seesaw models as examples of the classification. The anomaly cancellation conditions in these models are also discussed.

  4. Structural and Functional Studies on the Marburg Virus GP2 Fusion Loop.

    PubMed

    Liu, Nina; Tao, Yisong; Brenowitz, Michael D; Girvin, Mark E; Lai, Jonathan R

    2015-10-01

    Marburg virus (MARV) and the ebolaviruses belong to the family Filoviridae (the members of which are filoviruses) that cause severe hemorrhagic fever. Infection requires fusion of the host and viral membranes, a process that occurs in the host cell endosomal compartment and is facilitated by the envelope glycoprotein fusion subunit, GP2. The N-terminal fusion loop (FL) of GP2 is a hydrophobic disulfide-bonded loop that is postulated to insert and disrupt the host endosomal membrane during fusion. Here, we describe the first structural and functional studies of a protein corresponding to the MARV GP2 FL. We found that this protein undergoes a pH-dependent conformational change, as monitored by circular dichroism and nuclear magnetic resonance. Furthermore, we report that, under low pH conditions, the MARV GP2 FL can induce content leakage from liposomes. The general aspects of this pH-dependent structure and lipid-perturbing behavior are consistent with previous reports on Ebola virus GP2 FL. However, nuclear magnetic resonance studies in lipid bicelles and mutational analysis indicate differences in structure exist between MARV and Ebola virus GP2 FL. These results provide new insight into the mechanism of MARV GP2-mediated cell entry.

  5. Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.

    PubMed

    Pais, Tiago M; Lamosa, Pedro; dos Santos, Wagner; Legall, Jean; Turner, David L; Santos, Helena

    2005-02-01

    Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.

  6. Fields induced by three-dimensional dislocation loops in anisotropic magneto-electro-elastic bimaterials

    NASA Astrophysics Data System (ADS)

    Han, Xueli; Pan, Ernie; Sangghaleh, Ali

    2013-08-01

    The coupled elastic, electric and magnetic fields produced by an arbitrarily shaped three-dimensional dislocation loop in general anisotropic magneto-electro-elastic (MEE) bimaterials are derived. First, we develop line-integral expressions for the fields induced by a general dislocation loop. Then, we obtain analytical solutions for the fields, including the extended Peach-Koehler force, due to some useful dislocation segments such as straight line and elliptic arc. The present solutions contain the piezoelectric, piezomagnetic and purely elastic solutions as special cases. As numerical examples, the fields induced by a square and an elliptic dislocation loop in MEE bimaterials are studied. Our numerical results show the coupling effects among different fields, along with various interesting features associated with the dislocation and interface.

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

    PubMed Central

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

    1996-01-01

    Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with

  8. Introducing a Rigid Loop Structure from Deer into Mouse Prion Protein Increases Its Propensity for Misfolding In Vitro

    PubMed Central

    Kyle, Leah M.; John, Theodore R.; Schätzl, Hermann M.; Lewis, Randolph V.

    2013-01-01

    Prion diseases are fatal neurodegenerative disorders characterized by misfolding of the cellular prion protein (PrPc) into the disease-associated isoform (PrPSc) that has increased β-sheet content and partial resistance to proteolytic digestion. Prion diseases from different mammalian species have varying propensities for transmission upon exposure of an uninfected host to the infectious agent. Chronic Wasting Disease (CWD) is a highly transmissible prion disease that affects free ranging and farmed populations of cervids including deer, elk and moose, as well as other mammals in experimental settings. The molecular mechanisms allowing CWD to maintain comparatively high transmission rates have not been determined. Previous work has identified a unique structural feature in cervid PrP, a rigid loop between β-sheet 2 and α-helix 2 on the surface of the protein. This study was designed to test the hypothesis that the rigid loop has a direct influence on the misfolding process. The rigid loop was introduced into murine PrP as the result of two amino acid substitutions: S170N and N174T. Wild-type and rigid loop murine PrP were expressed in E. coli and purified. Misfolding propensity was compared for the two proteins using biochemical techniques and cell free misfolding and conversion systems. Murine PrP with a rigid loop misfolded in cell free systems with greater propensity than wild type murine PrP. In a lipid-based conversion assay, rigid loop PrP converted to a PK resistant, aggregated isoform at lower concentrations than wild-type PrP. Using both proteins as substrates in real time quaking-induced conversion, rigid loop PrP adopted a misfolded isoform more readily than wild type PrP. Taken together, these findings may help explain the high transmission rates observed for CWD within cervids. PMID:23825561

  9. Global structure of curves from generalized unitarity cut of three-loop diagrams

    NASA Astrophysics Data System (ADS)

    Hauenstein, Jonathan D.; Huang, Rijun; Mehta, Dhagash; Zhang, Yang

    2015-02-01

    This paper studies the global structure of algebraic curves defined by generalized unitarity cut of four-dimensional three-loop diagrams with eleven propagators. The global structure is a topological invariant that is characterized by the geometric genus of the algebraic curve. We use the Riemann-Hurwitz formula to compute the geometric genus of algebraic curves with the help of techniques involving convex hull polytopes and numerical algebraic geometry. Some interesting properties of genus for arbitrary loop orders are also explored where computing the genus serves as an initial step for integral or integrand reduction of three-loop amplitudes via an algebraic geometric approach.

  10. The Effect of Loops on the Structural Organization of α-Helical Membrane Proteins

    PubMed Central

    Tastan, Oznur; Klein-Seetharaman, Judith; Meirovitch, Hagai

    2009-01-01

    Loops connecting the transmembrane (TM) α-helices in membrane proteins are expected to affect the structural organization of the thereby connected helices and the helical bundles as a whole. This effect, which has been largely ignored previously, is studied here by analyzing the x-ray structures of 41 α-helical membrane proteins. First we define the loop flexibility ratio, R, and find that 53% of the loops are stretched, where a stretched loop constrains the distance between the two connected helices. The significance of this constraining effect is supported by experiments carried out with bacteriorhodopsin and rhodopsin, in which cutting or eliminating their (predominately stretched) loops has led to a decrease in protein stability, and for rhodopsin, in most cases, also to the destruction of the structure. We show that for nonstretched loops in the extramembranous regions, the fraction of hydrophobic residues is comparable to that for soluble proteins; furthermore (as is also the case for soluble proteins), the hydrophobic residues in these regions are preferentially buried. This is expected to lead to the compact structural organization of the loops, which is transferred to the TM helices, causing them to assemble. We argue that a soluble protein complexed with a membrane protein similarly promotes compactness; other properties of such complexes are also studied. We calculate complementary attractive interactions between helices, including hydrogen bonds and van der Waals interactions of sequential motifs, such as GXXXG. The relative and combined effects of all these factors on the association of the TM helices are discussed and protein structures with only a few of these factors are analyzed. Our study emphasizes the need for classifying membrane proteins into groups according to structural organization. This classification should be considered when procedures for structural analysis or prediction are developed and applied. Detailed analysis of each structure

  11. ArchDB: automated protein loop classification as a tool for structural genomics.

    PubMed

    Espadaler, Jordi; Fernandez-Fuentes, Narcis; Hermoso, Antonio; Querol, Enrique; Aviles, Francesc X; Sternberg, Michael J E; Oliva, Baldomero

    2004-01-01

    The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-secondary structural motifs, consisting of a few secondary structures and their connecting loops. Moreover, protein loops play an important role in protein function. Here we present ArchDB, a classification database of structural motifs, consisting of one loop plus its bracing secondary structures. ArchDB currently contains 12,665 super-secondary elements classified into 1496 motif subclasses. The database provides an easy way to retrieve functional information from protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, or to search by keywords on proteins with classified loops. The ArchDB database of loops is located at http://sbi.imim.es/archdb. PMID:14681390

  12. A light-induced shortcut in the planktonic microbial loop.

    PubMed

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A; Calbet, Albert; Nejstgaard, Jens C; Gasol, Josep M; Isari, Stamatina; Moorthi, Stefanie D; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F; Tsagaraki, Tatiana M; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-01-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light. PMID:27404551

  13. A light-induced shortcut in the planktonic microbial loop

    PubMed Central

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A.; Calbet, Albert; Nejstgaard, Jens C.; Gasol, Josep M.; Isari, Stamatina; Moorthi, Stefanie D.; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F.; Tsagaraki, Tatiana M.; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D.; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A.; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-01-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light. PMID:27404551

  14. Unresolved fine-scale structure in solar coronal loop-tops

    SciTech Connect

    Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.; Antolin, P.

    2014-12-10

    New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certain circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.

  15. Dislocation dynamics simulations of interactions between gliding dislocations and radiation induced prismatic loops in zirconium

    NASA Astrophysics Data System (ADS)

    Drouet, Julie; Dupuy, Laurent; Onimus, Fabien; Mompiou, Frédéric; Perusin, Simon; Ambard, Antoine

    2014-06-01

    The mechanical behavior of Pressurized Water Reactor fuel cladding tubes made of zirconium alloys is strongly affected by neutron irradiation due to the high density of radiation induced dislocation loops. In order to investigate the interaction mechanisms between gliding dislocations and loops in zirconium, a new nodal dislocation dynamics code, adapted to Hexagonal Close Packed metals, has been used. Various configurations have been systematically computed considering different glide planes, basal or prismatic, and different characters, edge or screw, for gliding dislocations with -type Burgers vectors. Simulations show various interaction mechanisms such as (i) absorption of a loop on an edge dislocation leading to the formation of a double super-jog, (ii) creation of a helical turn, on a screw dislocation, that acts as a strong pinning point or (iii) sweeping of a loop by a gliding dislocation. It is shown that the clearing of loops is more favorable when the dislocation glides in the basal plane than in the prismatic plane explaining the easy dislocation channeling in the basal plane observed after neutron irradiation by transmission electron microscopy.

  16. Structural Basis for Inactivation of the Human Pyruvate Dehydrogenase Complex by Phosphorylation: Role of Disordered Phosphorylation Loops

    SciTech Connect

    Kato, Masato; Wynn, R. Max; Chuang, Jacinta L.; Tso, Shih-Chia; Machius, Mischa; Li, Jun; Chuang, David T.

    2009-09-11

    We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-{alpha} (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-{alpha} prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-{alpha}, which nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.

  17. The application of cluster analysis in the intercomparison of loop structures in RNA.

    PubMed

    Huang, Hung-Chung; Nagaswamy, Uma; Fox, George E

    2005-04-01

    We have developed a computational approach for the comparison and classification of RNA loop structures. Hairpin or interior loops identified in atomic resolution RNA structures were intercompared by conformational matching. The root-mean-square deviation (RMSD) values between all pairs of RNA fragments of interest, even if from different molecules, are calculated. Subsequently, cluster analysis is performed on the resulting matrix of RMSD distances using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis objectively reveals groups of folds that resemble one another. To demonstrate the utility of the approach, a comprehensive analysis of all the terminal hairpin tetraloops that have been observed in 15 RNA structures that have been determined by X-ray crystallography was undertaken. The method found major clusters corresponding to the well-known GNRA and UNCG types. In addition, two tetraloops with the unusual primary sequence UMAC (M is A or C) were successfully assigned to the GNRA cluster. Larger loop structures were also examined and the clustering results confirmed the occurrence of variations of the GNRA and UNCG tetraloops in these loops and provided a systematic means for locating them. Nineteen examples of larger loops that closely resemble either the GNRA or UNCG tetraloop were found in the large ribosomal RNAs. When the clustering approach was extended to include all structures in the SCOR database, novel relationships were detected including one between the ANYA motif and a less common folding of the GAAA tetraloop sequence.

  18. Structure of a cardiotoxic phospholipase A(2) from Ophiophagus hannah with the "pancreatic loop".

    PubMed

    Zhang, Hai-Long; Xu, Su-Juan; Wang, Qiu-Yan; Song, Shi-Ying; Shu, Yu-Yan; Lin, Zheng-Jiong

    2002-06-01

    The crystal structure of an acidic phospholipase A(2) from Ophiophagus hannah (king cobra) has been determined by molecular replacement at 2.6-A resolution to a crystallographic R factor of 20.5% (R(free)=23.3%) with reasonable stereochemistry. The venom enzyme contains an unusual "pancreatic loop." The conformation of the loop is well defined and different from those in pancreas PLA(2), showing its structural variability. This analysis provides the first structure of a PLA(2)-type cardiotoxin. The sites related to the cardiotoxic and myotoxic activities are explored and the oligomer observed in the crystalline state is described. PMID:12217659

  19. Strain-induced electrostatic enhancements of BiFeO3 nanowire loops.

    PubMed

    Liu, Jun; Prashanthi, Kovur; Li, Zhi; McGee, Ryan T; Ahadi, Kaveh; Thundat, Thomas

    2016-08-17

    Semiconductor nanowires (NWs), due to their intriguing structural and physical properties, offer tremendous potential for future technological applications. The existence of strain in NWs can greatly affect, for instance, their mechanical, electrical and optical properties. Here, we report an extraordinary electrostatic response of semiconductor BiFeO3 NW loops, based on Kelvin probe force microscopy (KPFM) and electrostatic force microscopy (EFM). A substantial ∼300 mV surface potential difference, accompanied by an ∼29% higher surface charge density, was found on the NW loop. We also found that the electrostatic enhancement is strongly related to the strain present at the curvature of the NW loops. We propose that the electric polarization coupled with mechanical strain (piezoelectric effect) or strain gradient (flexoelectricity) as possible reasons to account for our observation. These findings provide new insights into multiferroic based semiconductor NWs under external stimuli as well as significant inspiration towards strain sensors and electromechanical devices with multifunctional sensing abilities. PMID:27477993

  20. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.

    PubMed

    Jiang, Fuguo; Taylor, David W; Chen, Janice S; Kornfeld, Jack E; Zhou, Kaihong; Thompson, Aubri J; Nogales, Eva; Doudna, Jennifer A

    2016-02-19

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation.

  1. Crystal Structures and Molecular Dynamics Simulations of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion for Co-Substrate Binding

    PubMed Central

    Luo, Huei-Ru; Wu, Szu-Pei; Hsu, Chun-Hua

    2013-01-01

    Malate dehydrogenase (MDH) catalyzes the conversion of oxaloacetate and malate by using the NAD/NADH coenzyme system. The system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. We elucidated the biochemical and structural features of MDH from Thermus thermophilus (TtMDH) for use in various biotechnological applications. The biochemical characterization of recombinant TtMDH revealed greatly increased activity above 60°C and specific activity of about 2,600 U/mg with optimal temperature of 90°C. Analysis of crystal structures of apo and NAD-bound forms of TtMDH revealed a slight movement of the binding loop and few structural elements around the co-substrate binding packet in the presence of NAD. The overall structures did not change much and retained all related positions, which agrees with the CD analyses. Further molecular dynamics (MD) simulation at higher temperatures were used to reconstruct structures from the crystal structure of TtMDH. Interestingly, at the simulated structure of 353 K, a large change occurred around the active site such that with increasing temperature, a mobile loop was closed to co-substrate binding region. From biochemical characterization, structural comparison and MD simulations, the thermal-induced conformational change of the co-substrate binding loop of TtMDH may contribute to the essential movement of the enzyme for admitting NAD and may benefit the enzyme's activity. PMID:24386145

  2. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

    PubMed Central

    Stork, Caroline Townsend; Bocek, Michael; Crossley, Madzia P; Sollier, Julie; Sanz, Lionel A; Chédin, Frédéric; Swigut, Tomek; Cimprich, Karlene A

    2016-01-01

    The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability, and elevated E2 levels are tied to breast cancer. Here, we show that E2 stimulation causes a rapid, global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some instances have been linked to DNA damage. We show that E2-dependent R-loop formation and breast cancer rearrangements are highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility. DOI: http://dx.doi.org/10.7554/eLife.17548.001 PMID:27552054

  3. A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

    PubMed Central

    Gangwar, Deepti; Kalita, Mridul K; Gupta, Dinesh; Chauhan, Virander S; Mohmmed, Asif

    2009-01-01

    Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B) are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s) for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from the parasite that could

  4. Curcumin improves synaptic plasticity impairment induced by HIV-1gp120 V3 loop

    PubMed Central

    Shen, Ling-ling; Jiang, Ming-liang; Liu, Si-si; Cai, Min-chun; Hong, Zhong-qiu; Lin, Li-qing; Xing, Yan-yan; Chen, Gui-lin; Pan, Rui; Yang, Li-juan; Xu, Ying; Dong, Jun

    2015-01-01

    Curcumin has been shown to significantly improve spatial memory impairment induced by HIV-1 gp120 V3 in rats, but the electrophysiological mechanism remains unknown. Using extracellular microelectrode recording techniques, this study confirmed that the gp120 V3 loop could suppress long-term potentiation in the rat hippocampal CA1 region and synaptic plasticity, and that curcumin could antagonize these inhibitory effects. Using a Fura-2/AM calcium ion probe, we found that curcumin resisted the effects of the gp120 V3 loop on hippocampal synaptosomes and decreased Ca2+ concentration in synaptosomes. This effect of curcumin was identical to nimodipine, suggesting that curcumin improved the inhibitory effects of gp120 on synaptic plasticity, ameliorated damage caused to the central nervous system, and might be a potential neuroprotective drug. PMID:26199609

  5. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine

    PubMed Central

    Dishler, Abigael L.; McMichael, Elizabeth L.; Serra, Martin J.

    2015-01-01

    Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5′ or 3′ position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5′ or 3′ side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures. PMID:25805856

  6. Dangling bond deflection model: Growth of gel network with loop structure

    NASA Astrophysics Data System (ADS)

    Ma, Hang-Shing; Jullien, Rémi; Scherer, George W.

    2002-04-01

    It has been shown that the closed-loop structure in the model gel networks is responsible for their stiffness. However, the creation of loops has been underestimated in most of the existing kinetic aggregation models [e.g., DLCA (diffusion-limited cluster-cluster aggregation) and derivatives]. A dangling bond deflection (DEF) mechanism is proposed to model the fluctuation of dangling branches or dead ends under thermal excitation. The random deflections of the dangling branches can create loops in the network by forming intracluster bonds, and proceed during both the gelling and aging processes. The resulting DLCADEF networks have extensive loop structure with a negligible number of dangling branches. Its growth kinetics and fractal behavior resemble those of real gels, including volume-invariant gel time and fractal dimension of about 2. The DLCADEF model is the first attempt to model the gel growth with loop formation by the physically realistic fluctuation mechanism. The mechanical properties of the resulting networks will be studied and verified by comparison with real gels.

  7. A genetic algorithm based molecular modeling technique for RNA stem-loop structures.

    PubMed Central

    Ogata, H; Akiyama, Y; Kanehisa, M

    1995-01-01

    A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position. Images PMID:7533901

  8. [Structural and functional findings in experimental blind loop syndrome].

    PubMed

    Riecken, E O

    1984-01-01

    Proximal and distal the blindsack a villus and crypt prolongation connected with a decreasing absorption of octanoate could be pointed out. The structural changes are very likely a hyperplasia of the mucosa. Within the blindsack a hyperplasia in connection with an accelerated proliferation of cells and an almost three and a halffold enlargement of the surface of the villi could be found. Simultaneously, the mucosa was damaged. An artificial bile duct as well as a neomycin therapy caused a decrease of the structural and functional changes but did not prevent the mucosal hyperplasia. These results are explained with adaptive processes of the small intestinal mucosa in a sense of hyperregeneration alterations of sprue typus.

  9. Closed-loop structural stability for linear-quadratic optimal systems

    NASA Technical Reports Server (NTRS)

    Wong, P. K.; Athans, M.

    1975-01-01

    This paper contains an explicit parameterization of a subclass of linear constant gain feedback maps that never destabilize an originally open-loop stable system. These results can then be used to obtain several new structural stability results for multi-input linear-quadratic feedback optimal designs.

  10. Towards the use of Structural Loop Analysis to Study System Behaviour of Socio-Ecological Systems.

    NASA Astrophysics Data System (ADS)

    Abram, Joseph; Dyke, James

    2016-04-01

    Maintaining socio-ecological systems in desirable states is key to developing a growing economy, alleviating poverty and achieving a sustainable future. While the driving forces of an environmental system are often well known, the dynamics impacting these drivers can be hidden within a tangled structure of causal chains and feedback loops. A lack of understanding of a system's dynamic structure and its influence on a system's behaviour can cause unforeseen side-effects during model scenario testing and policy implementation. Structural Loop analysis of socio-ecological system models identifies dominant feedback structures during times of behavioural shift, allowing the user to monitor key influential drivers during model simulation. This work carries out Loop Eigenvalue Elasticity Analysis (LEEA) on three system dynamic models, exploring tipping points in lake systems undergoing eutrophication. The purpose is to explore the potential benefits and limitations of the technique in the field of socio-ecology. The LEEA technique shows promise for socio-ecological systems which undergo regime shifts or express oscillatory trends, but shows limited usefulness with large models. The results of this work highlight changes in feedback loop dominance, years prior to eutrophic tipping events in lake systems. LEEA could be used as an early warning signal to impending system changes, complementary to other known early warning signals. This approach could improve our understanding during critical times of a system's behaviour, changing how we approach model analysis and the way scenario testing and policy implementation are addressed in socio-ecological system models.

  11. Structure and function of the third intracellular loop of the 5-hydroxytryptamine2A receptor: the third intracellular loop is alpha-helical and binds purified arrestins.

    PubMed

    Gelber, E I; Kroeze, W K; Willins, D L; Gray, J A; Sinar, C A; Hyde, E G; Gurevich, V; Benovic, J; Roth, B L

    1999-05-01

    Understanding the precise structure and function of the intracellular domains of G protein-coupled receptors is essential for understanding how receptors are regulated, and how they transduce their signals from the extracellular milieu to intracellular sites. To understand better the structure and function of the intracellular domain of the 5-hydroxytryptamine2A (5-HT2A) receptor, a model G(alpha)q-coupled receptor, we overexpressed and purified to homogeneity the entire third intracellular loop (i3) of the 5-HT2A receptor, a region previously implicated in G-protein coupling. Circular dichroism spectroscopy of the purified i3 protein was consistent with alpha-helical and beta-loop, -turn, and -sheet structure. Using random peptide phage libraries, we identified several arrestin-like sequences as i3-interacting peptides. We subsequently found that all three known arrestins (beta-arrestin, arrestin-3, and visual arrestin) bound specifically to fusion proteins encoding the i3 loop of the 5-HT(2A) receptor. Competition binding studies with synthetic and recombinant peptides showed that the middle portion of the i3 loop, and not the extreme N and C termini, was likely to be involved in i3-arrestin interactions. Dual-label immunofluorescence confocal microscopic studies of rat cortex indicated that many cortical pyramidal neurons coexpressed arrestins (beta-arrestin or arrestin-3) and 5-HT2A receptors, particularly in intracellular vesicles. Our results demonstrate (a) that the i3 loop of the 5-HT2A receptor represents a structurally ordered domain composed of alpha-helical and beta-loop, -turn, and -sheet regions, (b) that this loop interacts with arrestins in vitro, and is hence active, and (c) that arrestins are colocalized with 5-HT2A receptors in vivo.

  12. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.

    PubMed

    Tran, Huyen Thi; Hong, Myoung Ki; Ngo, Ho Phuong Thuy; Huynh, Kim Hung; Ahn, Yeh Jin; Wang, Zhong; Kang, Lin Woo

    2016-01-01

    D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.

  13. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.

    PubMed

    Tran, Huyen Thi; Hong, Myoung Ki; Ngo, Ho Phuong Thuy; Huynh, Kim Hung; Ahn, Yeh Jin; Wang, Zhong; Kang, Lin Woo

    2016-01-01

    D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops. PMID:26894530

  14. Proximity effect induced magnetoresistance hysteresis loops in a topological insulator/YIG heterostructure

    NASA Astrophysics Data System (ADS)

    Montazeri, Mohammad; Lang, Murong; Onbasli, Mehmet C.; Kou, Xufeng; He, Liang; Ross, Caroline A.; Wang, Kang L.

    2014-03-01

    We experimentally demonstrate the proximity effect induced hysteretic magnetoresistance in an 8 quintuple layers of Bi2Se3 films grown on Gallium Gadolinium Garnet (GGG) (111) substrates with a 50 nm Yttrium Iron Garnet (YIG) buffer layer by molecular beam epitaxy. With in-plane and out-of-plane magnetic field, square wave shaped and butterfly shaped resistance hysteresis loops can be observed up to 25 K, respectively. The relationship between the hysteretic MR curves and the magnetic switching of the YIG will be discussed in the context of a proximity effect between the YIG and the TI.

  15. Closed-Loop Performance Measures for Flight Controllers Subject to Neutron-Induced Upsets

    NASA Technical Reports Server (NTRS)

    Gray, W. Steven; Zhang, Hong; Gonzalex, Oscar R.

    2003-01-01

    It has been observed that atmospheric neutrons can produce single event upsets in digital flight control hardware. The phenomenon has been studied extensively at the chip level, and now system level experiments are underway. In this paper analytical closed-loop performance measures for the tracking error are developed for a plant that is stabilized by a recoverable computer system subject to neutron induced upsets. The underlying model is a Markov jump-linear system with process noise. The steady-state tracking error is expressed in terms of a generalized observability Gramian.

  16. Post-flare loops embedded in a hot coronal fan-like structure

    NASA Technical Reports Server (NTRS)

    Svestka, Z.; Farnik, F.; Hudson, H. S.; Hick, P.

    1997-01-01

    Limb events were demonstrated on the sun in which rising post-flare loops were embedded in hot structures looking in soft X-rays like fans of rays, formed during the flare and extending high into the corona. One of these structures is analyzed and it is suggested that these fans of rays represent temporary ministreamers, along which mass flows into interplanetary space. This suggestion is supported by maps of solar wind density constructed from scintillation measurements.

  17. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

    PubMed Central

    Bonneau, Eric; Girard, Nicolas; Boisbouvier, Jérôme; Legault, Pascale

    2011-01-01

    The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme. PMID:21266483

  18. Structural Variation and Uniformity among Tetraloop-Receptor Interactions and Other Loop-Helix Interactions in RNA Crystal Structures

    PubMed Central

    Wu, Li; Chai, Dinggeng; Fraser, Marie E.; Zimmerly, Steven

    2012-01-01

    Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the “standard” GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature. PMID:23152878

  19. Soft X-ray imaging of the TY Pyx binary system - II. Modelling the interconnecting loop-like structure

    NASA Astrophysics Data System (ADS)

    Pres, Pawel; Siarkowski, Marek; Sylwester, Janusz

    1995-07-01

    In this paper we present improved results of 3D deconvolution of the TY Pyx LEIT light curve, taking into account the effect of `halo' emission. The results obtained indicate that the bulk of plasma is between the two stars. The spatial distribution of the emission suggests the presence of the loop structure interconnecting the stars, as was argued in the previous paper by Siarkowski, Sylwester & Pres. We have modelled the physical conditions in this loop using the hydrostatic coronal loop model presented by Vesecky, Antiochos & Underwood. The brightness distribution along this interconnecting structure can be interpreted by loop models with 1215.

  20. Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations.

    PubMed

    Dai, Liang; Zhou, Yaoqi

    2011-05-01

    Worldwide structural genomics projects are increasing structure coverage of sequence space but have not significantly expanded the protein structure space itself (i.e., number of unique structural folds) since 2007. Discovering new structural folds experimentally by directed evolution and random recombination of secondary-structure blocks is also proved rarely successful. Meanwhile, previous computational efforts for large-scale mapping of protein structure space are limited to simple model proteins and led to an inconclusive answer on the completeness of the existing observed protein structure space. Here, we build novel protein structures by extending naturally occurring circular (single-loop) permutation to multiple loop permutations (MLPs). These structures are clustered by structural similarity measure called TM-score. The computational technique allows us to produce different structural clusters on the same naturally occurring, packed, stable core but with alternatively connected secondary-structure segments. A large-scale MLP of 2936 domains from structural classification of protein domains reproduces those existing structural clusters (63%) mostly as hubs for many nonredundant sequences and illustrates newly discovered novel clusters as islands adopted by a few sequences only. Results further show that there exist a significant number of novel potentially stable clusters for medium-size or large-size single-domain proteins, in particular, >100 amino acid residues, that are either not yet adopted by nature or adopted only by a few sequences. This study suggests that MLP provides a simple yet highly effective tool for engineering and design of novel protein structures (including naturally knotted proteins). The implication of recovering new-fold targets from critical assessment of structure prediction techniques (CASP) by MLP on template-based structure prediction is also discussed. Our MLP structures are available for download at the publication page of the

  1. Frequency-induced changes in interlimb interactions: increasing manifestations of closed-loop control.

    PubMed

    de Boer, Betteco J; Peper, C Lieke E; Beek, Peter J

    2011-06-20

    In bimanual coordination, interactions between the limbs result in attraction to in-phase and antiphase coordination. Increasing movement frequency leads to decreasing stability of antiphase coordination, often resulting in a transition to the more stable in-phase pattern. It is unknown, however, how this frequency-induced loss of stability is engendered in terms of the interlimb interactions underwriting bimanual coordination. The present study was conducted to help resolve this issue. Using an established method (based on comparison of various unimanual and bimanual tasks involving both passive and active movements), three sources of interlimb interaction were dissociated: (1) integrated timing of feedforward signals, (2) afference-based correction of relative phase errors, and (3) phase entrainment by contralateral afference. Results indicated that phase entrainment strength remained unaffected by frequency and that the stabilizing effects of error correction and integrated timing decreased with increasing frequency. Their contributions, however, reflected an interesting interplay as frequency increased. For moderate frequencies coordinative stability was predominantly secured by integrated timing processes. However, at high frequencies, the stabilization of the antiphase pattern required combined contributions of both integrated timing and error correction. In sum, increasing frequency was found to induce a shift from predominantly open-loop control to more closed-loop control. The results may be accounted for by means of an internal forward model for sensorimotor integration in which the sensory signals are compared to values predicted on the basis of efference copies.

  2. TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop.

    PubMed

    Settembre, Carmine; De Cegli, Rossella; Mansueto, Gelsomina; Saha, Pradip K; Vetrini, Francesco; Visvikis, Orane; Huynh, Tuong; Carissimo, Annamaria; Palmer, Donna; Klisch, Tiemo Jürgen; Wollenberg, Amanda C; Di Bernardo, Diego; Chan, Lawrence; Irazoqui, Javier E; Ballabio, Andrea

    2013-06-01

    The lysosomal-autophagic pathway is activated by starvation and plays an important role in both cellular clearance and lipid catabolism. However, the transcriptional regulation of this pathway in response to metabolic cues is uncharacterized. Here we show that the transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, is induced by starvation through an autoregulatory feedback loop and exerts a global transcriptional control on lipid catabolism via Ppargc1α and Ppar1α. Thus, during starvation a transcriptional mechanism links the autophagic pathway to cellular energy metabolism. The conservation of this mechanism in Caenorhabditis elegans suggests a fundamental role for TFEB in the evolution of the adaptive response to food deprivation. Viral delivery of TFEB to the liver prevented weight gain and metabolic syndrome in both diet-induced and genetic mouse models of obesity, suggesting a new therapeutic strategy for disorders of lipid metabolism.

  3. The basic helix-loop-helix transcription factor, Mist1, induces maturation of mouse fetal hepatoblasts.

    PubMed

    Chikada, Hiromi; Ito, Keiichi; Yanagida, Ayaka; Nakauchi, Hiromitsu; Kamiya, Akihide

    2015-10-12

    Hepatic stem/progenitor cells, hepatoblasts, have a high proliferative ability and can differentiate into mature hepatocytes and cholangiocytes. Therefore, these cells are considered to be useful for regenerative medicine and drug screening for liver diseases. However, it is problem that in vitro maturation of hepatoblasts is insufficient in the present culture system. In this study, a novel regulator to induce hepatic differentiation was identified and the molecular function of this factor was examined in embryonic day 13 hepatoblast culture with maturation factor, oncostatin M and extracellular matrices. Overexpression of the basic helix-loop-helix type transcription factor, Mist1, induced expression of mature hepatocytic markers such as carbamoyl-phosphate synthetase1 and several cytochrome P450 (CYP) genes in this culture system. In contrast, Mist1 suppressed expression of cholangiocytic markers such as Sox9, Sox17, Ck19, and Grhl2. CYP3A metabolic activity was significantly induced by Mist1 in this hepatoblast culture. In addition, Mist1 induced liver-enriched transcription factors, CCAAT/enhancer-binding protein α and Hepatocyte nuclear factor 1α, which are known to be involved in liver functions. These results suggest that Mist1 partially induces mature hepatocytic expression and function accompanied by the down-regulation of cholangiocytic markers.

  4. Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

    PubMed Central

    Das, Rhiju

    2013-01-01

    Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC) Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a ‘stepwise ansatz’, recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA) protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth ‘RNA-puzzle’ competition. These results establish all-atom enumeration as an

  5. Structural Insights into the Role of Architectural Proteins in DNA Looping Deduced from Computer Simulations

    PubMed Central

    Olson, Wilma K.; Grosner, Michael A.; Czapla, Luke; Swigon, David

    2013-01-01

    Bacterial gene expression is regulated by DNA elements that often lie far apart along the genomic sequence but come close together during genetic processing. The intervening residues form loops, which are organized by the binding of various proteins. For example, the Escherichia coli Lac repressor protein binds DNA operators, separated by 92 or 401 base pairs, and suppresses the formation of gene products involved in the metabolism of lactose. The system also includes several highly abundant architectural proteins, such as the histone-like (heat unstable) HU protein, which severely deform the double helix upon binding. In order to gain a better understanding of how the naturally stiff DNA double helix forms the short loops detected in vivo, we have developed new computational methods to study the effects of various non-specifically binding proteins on the three-dimensional configurational properties of DNA sequences. This article surveys the approach that we use to generate ensembles of spatially constrained protein-decorated DNA structures (minicircles and Lac repressor-mediated loops) and presents some of the insights gained from the correspondence between computation and experiment about the potential contributions of architectural and regulatory proteins to DNA looping and gene expression. PMID:23514154

  6. Localization of Magnetic Field Structure of Multi-Current Loops on Axisymmetrical Model for Transcranial Magnetic Stimulation

    NASA Astrophysics Data System (ADS)

    Okita, Taishi; Takagi, Toshiyuki

    2009-01-01

    We calculate magnetic field distributions from multi-current loops for transcranial magnetic stimulation (TMS). In TMS, it is important to produce locally strong magnetic fields and apply eddy-currents only to the aimed cell in a deep region of the brain. First, we investigate the field structure around a single current loop. We find that a single loop generates the convexed field on a certain plane parallel to the loop surface. Second, we study an axisymmetrical model of three-current loops, i.e., a main-coil and two sub-coils, in which the fields are significantly localized in the vertical direction at a symmetrical plane on the central axis compared with that of a single loop.

  7. Modulated drug release from the stem-and-loop structured oligodeoxynucleotide upon UV-A irradiation in the presence of target DNA.

    PubMed

    Tanabe, Kazuhito; Nakata, Hiroyuki; Mukai, Shin; Nishimoto, Sei-ichi

    2005-11-01

    o-Nitrobenzyl photochemistry as induced by UV-A irradiation was applied to a photoactivated drug releasing system based on a molecular beacon strategy. A stem-and-loop structured oligodeoxynucleotide (ODN) possessing a photoreactive o-nitrobenzyl chromophore at the 3'-end and 1-aminonaphthalene quencher at the 5'-end underwent conformational change into a conventional double strand structure by hybridization with a specified target DNA. The intrinsic stem-and-loop structure suppressed photoactivated release of benzoic acid as a phantom drug from the o-nitrobenzyl chromophore because of intramolecular quenching by the 1-aminonaphthalene unit in close proximity to the chromophore. Formation of the double strand structure in the presence of perfectly matched target DNA minimized occurrence of intramolecular quenching and thereby enhanced the photoactivated drug release.

  8. The Effective Field Theory of Large Scale Structures at two loops

    SciTech Connect

    Carrasco, John Joseph M.; Foreman, Simon; Green, Daniel; Senatore, Leonardo E-mail: sfore@stanford.edu E-mail: senatore@stanford.edu

    2014-07-01

    Large scale structure surveys promise to be the next leading probe of cosmological information. It is therefore crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbation theory for the weakly non-linear regime of dark matter, where correlation functions are computed in an expansion of the wavenumber k of a mode over the wavenumber associated with the non-linear scale k{sub NL}. Since most of the information is contained at high wavenumbers, it is necessary to compute higher order corrections to correlation functions. After the one-loop correction to the matter power spectrum, we estimate that the next leading one is the two-loop contribution, which we compute here. At this order in k/k{sub NL}, there is only one counterterm in the EFTofLSS that must be included, though this term contributes both at tree-level and in several one-loop diagrams. We also discuss correlation functions involving the velocity and momentum fields. We find that the EFTofLSS prediction at two loops matches to percent accuracy the non-linear matter power spectrum at redshift zero up to k∼ 0.6 h Mpc{sup −1}, requiring just one unknown coefficient that needs to be fit to observations. Given that Standard Perturbation Theory stops converging at redshift zero at k∼ 0.1 h Mpc{sup −1}, our results demonstrate the possibility of accessing a factor of order 200 more dark matter quasi-linear modes than naively expected. If the remaining observational challenges to accessing these modes can be addressed with similar success, our results show that there is tremendous potential for large scale structure surveys to explore the primordial universe.

  9. Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

    PubMed Central

    Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

    2014-01-01

    G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. PMID:24896119

  10. Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure

    PubMed Central

    Gardner, David P.; Ren, Pengyu; Ozer, Stuart; Gutell, Robin R.

    2011-01-01

    RNA is directly associated with a growing number of functions within the cell. The accurate prediction of different RNAs higher-order structure from their nucleic acid sequences will provide insight into their functions and molecular mechanics. We have been determining statistical potentials for a collection of structural elements that is larger than the number of structural elements determined with experimentally determined energy values. The experimentally derived free-energies and the statistical potentials for canonical base pair stacks are analogous, demonstrating that statistical potentials derived from comparative data can be used as an alternative energetic parameter. A new computational infrastructure - RNA Comparative Analysis Database (rCAD) - that utilizes a relational database was developed to manipulate and analyze very large sequence alignments and secondary structure datasets. Using rCAD, a richer set of energetic parameters for RNA fundamental structural elements including hairpin and internal loops was determined. A new version of RNAfold was developed to utilize these statistical potentials. Overall, these new statistical potentials for hairpin and internal loops integrated into the new version of RNAfold demonstrated significant improvements in the prediction accuracy of RNA secondary structure. PMID:21889515

  11. Empirical analysis of the spatial structure of meander evolution: Insights into the development of compound loops

    NASA Astrophysics Data System (ADS)

    Guneralp, I.; Rhoads, B. L.

    2009-12-01

    Complex meander forms such as compound loops or multi-lobes are common features of natural meandering rivers. Despite a large body of research on river meandering, the development of compound loops is not fully understood. An improved understanding of the development of compound loops is crucial due to the importance of planform migration dynamics in floodplain development and landscape evolution. Indeed, such an understanding would facilitate the mitigation of river hazards created by bank erosion and channel migration and help develop more effective river management strategies and sustainable river restoration practices. The purpose of this study is to explain the complex interactions between the planform curvature and migration dynamics that result in the development of compound loops. For this purpose, we evaluated empirically the effect of planform curvature on the migration dynamics of several natural meander-trains with varying degrees of planform complexity and a set of complex meander bends of a meander-train. In the analysis of the meander-trains, we employed a dynamical systems approach and used the capabilities of Discrete Signal Processing, which allows for the empirical derivation of the spatial relation between the planform curvature and migration rate. Data for the meander-trains extracted from multi-temporal aerial photography. In the analysis of the complex meander bends, we used phase-space diagrams developed using a refined version of an existing empirical-analysis method and newly developed analytical technique of planform characterization that overcome the limitations of past work. The results of the study suggest that the spatial structure of the curvature effect on the migration rate is complex, characterized by multiple behavior modes consisting of exponential decay as well as oscillatory structures. As the planform evolves to a complex geometry that contains compound loops, the dominant behavior mode changes from pure exponential decay to

  12. Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim.

    PubMed

    Darlington, T K; Wager-Smith, K; Ceriani, M F; Staknis, D; Gekakis, N; Steeves, T D; Weitz, C J; Takahashi, J S; Kay, S A

    1998-06-01

    The circadian oscillator generates a rhythmic output with a period of about 24 hours. Despite extensive studies in several model systems, the biochemical mode of action has not yet been demonstrated for any of its components. Here, the Drosophila CLOCK protein was shown to induce transcription of the circadian rhythm genes period and timeless. dCLOCK functioned as a heterodimer with a Drosophila homolog of BMAL1. These proteins acted through an E-box sequence in the period promoter. The timeless promoter contains an 18-base pair element encompassing an E-box, which was sufficient to confer dCLOCK responsiveness to a reporter gene. PERIOD and TIMELESS proteins blocked dCLOCK's ability to transactivate their promoters via the E-box. Thus, dCLOCK drives expression of period and timeless, which in turn inhibit dCLOCK's activity and close the circadian loop.

  13. An induced global magnetic field looping around the magnetotail of Venus

    NASA Astrophysics Data System (ADS)

    Chai, Lihui; Wei, Yong; Wan, Weixing; Zhang, Tielong; Rong, Zhaojin; Fraenz, Markus; Dubinin, Eduard; Zhang, Hui; Zhong, Jun; Han, Xiuhong; Barabash, Stas

    2016-01-01

    Venus serves as the prototype of solar wind interaction with unmagnetized planetary bodies with atmospheres. It has no intrinsic dipole or crustal magnetic field; the only magnetic field is believed to be formed by the draped interplanetary magnetic field (IMF). However, the large-scale magnetic field observed over the north polar region of Venus has a bias in the dawnward direction and seemingly unresponsive to the IMF's direction. Here we show that besides the draped field, there is a second type of induced global magnetic field at Venus and the dawnward field is only a part of it. This global field has a distribution in a cylindrical shell around the magnetotail and a counterclockwise direction looking from the planetary tail toward the Sun, which demonstrates that there are two currents flowing out and in of the planet along the inner and outer boundaries of the looping field, respectively.

  14. Single laser pulse induces spin state transition within the hysteresis loop of an Iron compound

    NASA Astrophysics Data System (ADS)

    Freysz, E.; Montant, S.; Létard, S.; Létard, J.-F.

    2004-08-01

    Within the thermal hysteresis loop of the [Fe(PM-BiA) 2(NCS) 2] compound, a single laser pulse of 14 mJ cm -2 induces a photo-conversion from the low spin (LS, S = 0) to the high spin (HS, S = 2) state of the Fe 2+ metallic center. The temporal dynamic of this phenomena indicates that the system is firstly photo-excited into the HS state and then slowly relaxes to a mixture of HS/LS state. Subsequent laser pulses do not affect the HS/LS ratio. The system can be brought back to its initial LS state by adjusting the temperature of the compound. A simple model accounts qualitatively for the observed phenomenon.

  15. An Induced Global Magnetic Field Looping Around the Magnetotail of Venus

    NASA Astrophysics Data System (ADS)

    Chai, Lihui; Wei, Yong; Wan, Weixing; Zhang, Tielong; Fraenz, Markus; Dubinin, Eduard; Zhang, Hui; Rong, Zhaojin; Barabash, Stas

    2016-04-01

    Venus serves as the prototype of solar wind interaction with unmagnetized planetary bodies with atmospheres. It has no intrinsic dipole or crustal magnetic field, the only magnetic field is believed to be formed by the draped interplanetary magnetic field (IMF). However, the large-scale magnetic field observed over the north polar region of Venus has a bias in the dawnward direction and seemingly unresponsive to the IMF's direction. Here we show that besides the draped field, there is a second type of induced global magnetic field at Venus, and the dawnward field is only a part of it. This global field has a distribution in a cylindrical shell around the magnetotail and a counterclockwise direction looking from the planetary tail toward the Sun, which demonstrates that there are two currents flowing out and in of the planet along the inner and outer boundaries of the looping field, respectively. [Chai et al., 2016, JGR, doi:10.1002/2015JA021904

  16. Polar structure of disclination loops in nematic liquid crystals probed by second-harmonic-light scattering.

    PubMed

    Pardaev, Shokir A; Williams, J C; Twieg, R J; Jakli, A; Gleeson, J T; Ellman, B; Sprunt, S

    2015-03-01

    Angle-resolved, second-harmonic-light scattering (SHLS) measurements are reported for three different classes of thermotropic nematic liquid crystals (NLCs): polar and nonpolar rodlike compounds and a bent-core compound. Results revealing well-defined scattering peaks are interpreted in terms of the electric polarization induced by distortions of the nematic orientational field ("flexopolarity") associated with inversion wall defects, nonsingular disclinations, analogous to Neel walls in ferromagnets, that often exhibit a closed loop morphology in NLCs. Analysis of the SHLS patterns based on this model provides a "proof-of-concept" for a potentially useful method to probe the flexopolar properties of NLCs.

  17. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.

    PubMed

    Wang, Shenlin; Ing, Christopher; Emami, Sanaz; Jiang, Yunjiang; Liang, Hongjun; Pomès, Régis; Brown, Leonid S; Ladizhansky, Vladimir

    2016-09-22

    Multiple moderate-resolution crystal structures of human aquaporin-1 have provided a foundation for understanding the molecular mechanism of selective water translocation in human cells. To gain insight into the interfacial structure and dynamics of human aquaporin-1 in a lipid environment, we performed nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulations. Using magic angle spinning solid-state NMR, we report a near complete resonance assignment of the human aquaporin-1. Chemical shift analysis of the secondary structure identified pronounced deviations from crystallographic structures in extracellular loops A and C, including the cis Y37-P38 bond in loop A, as well as ordering and immobilization of loop C. Site-specific H/D exchange measurements identify a number of protected nitrogen-bearing side chains and backbone amide groups, involved in stabilizing the loops. A combination of molecular dynamics simulations with NMR-derived restraints and filtering based on solvent accessibility allowed for the determination of a structural model of extracellular loops largely consistent with NMR results. The simulations reveal loop stabilizing interactions that alter the extracellular surface of human AQP1, with possible implications for water transport regulation through the channel. Modulation of water permeation may occur as a result of rearrangement of side chains from loop C in the extracellular vestibule of hAQP1, affecting the aromatic arginine selectivity filter. PMID:27583975

  18. Mapping the Structural and Dynamical Features of Multiple p53 DNA Binding Domains: Insights into Loop 1 Intrinsic Dynamics

    PubMed Central

    Lukman, Suryani; Lane, David P.; Verma, Chandra S.

    2013-01-01

    The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD). In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs). Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3). Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart). Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1) a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2) possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site. PMID:24324553

  19. Heat Removal from Bipolar Transistor by Loop Heat Pipe with Nickel and Copper Porous Structures

    PubMed Central

    Smitka, Martin; Malcho, Milan

    2014-01-01

    Loop heat pipes (LHPs) are used in many branches of industry, mainly for cooling of electrical elements and systems. The loop heat pipe is a vapour-liquid phase-change device that transfers heat from evaporator to condenser. One of the most important parts of the LHP is the porous wick structure. The wick structure provides capillary force to circulate the working fluid. To achieve good thermal performance of LHP, capillary wicks with high permeability and porosity and fine pore radius are expected. The aim of this work was to develop porous structures from copper and nickel powder with different grain sizes. For experiment copper powder with grain size of 50 and 100 μm and nickel powder with grain size of 10 and 25 μm were used. Analysis of these porous structures and LHP design are described in the paper. And the measurements' influences of porous structures in LHP on heat removal from the insulated gate bipolar transistor (IGBT) have been made. PMID:24959622

  20. Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Zhang, X.; Wang, J.

    2016-01-01

    Neutron and heavy ion irradiations generally induce voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacent to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.

  1. Defining the loop structures in proteins based on composite β-turn mimics.

    PubMed

    Dhar, Jesmita; Chakrabarti, Pinak

    2015-06-01

    Asx- and ω-turns are β-turn mimics, which replace the conventional main-chain hydrogen bonds seen in the latter by those involving the side chains, and both involve three residues. In this paper we analyzed the cases where these turns occur together--side by side, with or without any gap, overlapping and in any order. These composite turns (of length 3-15 residues), occurring at ∼1 per 100 residues, may constitute the full length of many loops, and when the residues in the two component turns overlap or are adjacent to each other, the composite may take well-defined shape. It is thus possible for non-regular regions in protein structure to form local structural motifs, akin to the regular geometrical features exhibited by secondary structures. Composites having the order ω-turns followed by Asx-turns can constitute N-terminal helix capping motif. Ternary composite turns (made up of ω-, Asx- and ST-turns), some with characteristic shape, have also been identified. Delineation of composite turns would help in characterizing loops in protein structures, which often have functional roles. Some sequence patterns seen in composites can be used for their incorporation in protein design.

  2. Non-perturbative corrections to the one-loop free energy induced by a massive scalar field on a stationary slowly varying in space gravitational background

    NASA Astrophysics Data System (ADS)

    Kalinichenko, Igor; Kazinski, Peter

    2014-08-01

    The explicit expressions for the one-loop non-perturbative corrections to the gravitational effective action induced by a scalar field on a stationary gravitational background are obtained both at zero and finite temperatures. The perturbative and non-perturbative contributions to the one-loop effective action are explicitly separated. It is proved that, after a suitable renormalization, the perturbative part of the effective action at zero temperature can be expressed in a covariant form solely in terms of the metric and its derivatives. This part coincides with the known large mass expansion of the one-loop effective action. The non-perturbative part of the renormalized one-loop effective action at zero temperature is proved to depend explicitly on the Killing vector defining the vacuum state of quantum fields. This part cannot be expressed in a covariant way through the metric and its derivatives alone. The implications of this result for the structure and symmetries of the effective action for gravity are discussed.

  3. R-loop induced stress response by second (p)ppGpp synthetase in Mycobacterium smegmatis: functional and domain interdependence.

    PubMed

    Krishnan, Sushma; Petchiappan, Anushya; Singh, Albel; Bhatt, Apoorva; Chatterji, Dipankar

    2016-10-01

    Persistent R-loops lead to replicative stress due to RNA polymerase stalling and DNA damage. RNase H enzymes facilitate the organisms to survive in the hostile condition by removing these R-loops. MS_RHII-RSD was previously identified to be the second (p)ppGpp synthetase in Mycobacterium smegmatis. The unique presence of an additional RNase HII domain raises an important question regarding the significance of this bifunctional protein. In this report, we demonstrate its ability to hydrolyze R-loops in Escherichia coli exposed to UV stress. MS_RHII-RSD gene expression was upregulated under UV stress, and this gene deleted strain showed increased R-loop accumulation as compared to the wild type. The domains in isolation are known to be inactive, and the full length protein is required for its function. Domain interdependence studies using active site mutants reveal the necessity of a hexamer form with high alpha helical content. In previous studies, bacterial RNase type HI has been mainly implicated in R-loop hydrolysis, but in this study, the RNase HII domain containing protein showed the activity. The prospective of this differential RNase HII activity is discussed. This is the first report to implicate a (p)ppGpp synthetase protein in R-loop-induced stress response.

  4. The integration of water loop heat pump and building structural thermal storage systems

    SciTech Connect

    Marseille, T.J.; Schliesing, J.S.

    1990-09-01

    Commercial buildings often have extensive periods where one space needs cooling and another heating. Even more common is the need for heating during one part of the day and cooling during another in the same spaces. If a building's heating and cooling system could be integrated with the building's structural mass such that the mass can be used to collect, store, and deliver energy, significant energy might be saved. Computer models were developed to simulate this interaction for an existing office building in Seattle, Washington that has a decentralized water-source heat pump system. Metered data available for the building was used to calibrate a base'' building model (i.e., nonintegrated) prior to simulation of the integrated system. In the simulated integration strategy a secondary water loop was manifolded to the main HVAC hydronic loop. tubing in this loop was embedded in the building's concrete floor slabs. Water was routed to this loop by a controller to charge or discharge thermal energy to and from the slabs. The slabs were also in thermal communication with the conditioned spaces. Parametric studies of the building model, using weather data for five other cities in addition to Seattle, predicted that energy can be saved on cooling dominated days. On hot, dry days and during the night the cooling tower can beneficially be used as a free cooling'' source for thermally charging'' the floor slabs using cooled water. Through the development of an adaptive/predictive control strategy, annual HVAC energy savings as large as 30% appear to be possible in certain climates. 8 refs., 13 figs.

  5. Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate

    PubMed Central

    Ababou, Abdessamad; Koronakis, Vassilis

    2016-01-01

    Gram-negative bacteria such as E. coli use tripartite efflux pumps such as AcrAB-TolC to expel antibiotics and noxious compounds. A key feature of the inner membrane transporter component, AcrB, is a short stretch of residues known as the gate/switch loop that divides the proximal and distal substrate binding pockets. Amino acid substitutions of the gate loop are known to decrease antibiotic resistance conferred by AcrB. Here we present two new AcrB gate loop variants, the first stripped of its bulky side chains, and a second in which the gate loop is removed entirely. By determining the crystal structures of the variant AcrB proteins in the presence and absence of erythromycin and assessing their ability to confer erythromycin tolerance, we demonstrate that the gate loop is important for AcrB export activity but is not required for erythromycin binding. PMID:27403665

  6. An interpretation of flare-induced and decayless coronal-loop oscillations as interference patterns

    SciTech Connect

    Hindman, Bradley W.; Jain, Rekha

    2014-04-01

    We present an alternative model of coronal-loop oscillations, which considers that the waves are trapped in a two-dimensional waveguide formed by the entire arcade of field lines. This differs from the standard one-dimensional model which treats the waves as the resonant oscillations of just the visible bundle of field lines. Within the framework of our two-dimensional model, the two types of oscillations that have been observationally identified, flare-induced waves and 'decayless' oscillations, can both be attributed to MHD fast waves. The two components of the signal differ only because of the duration and spatial extent of the source that creates them. The flare-induced waves are generated by strong localized sources of short duration, while the decayless background can be excited by a continuous, stochastic source. Further, the oscillatory signal arising from a localized, short-duration source can be interpreted as a pattern of interference fringes produced by waves that have traveled diverse routes of various pathlengths through the waveguide. The resulting amplitude of the fringes slowly decays in time with an inverse square root dependence. The details of the interference pattern depend on the shape of the arcade and the spatial variation of the Alfvén speed. The rapid decay of this wave component, which has previously been attributed to physical damping mechanisms that remove energy from resonant oscillations, occurs as a natural consequence of the interference process without the need for local dissipation.

  7. Structural delineation of stem-loop RNA binding by human TAF15 protein.

    PubMed

    Kashyap, Maruthi; Ganguly, Akshay Kumar; Bhavesh, Neel Sarovar

    2015-01-01

    Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence. PMID:26612539

  8. Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase

    PubMed Central

    Klein, Tobias; Vajpai, Navratna; Phillips, Jonathan J.; Davies, Gareth; Holdgate, Geoffrey A.; Phillips, Chris; Tucker, Julie A.; Norman, Richard A.; Scott, Andrew D.; Higazi, Daniel R.; Lowe, David; Thompson, Gary S.; Breeze, Alexander L.

    2015-01-01

    Protein tyrosine kinases differ widely in their propensity to undergo rearrangements of the N-terminal Asp–Phe–Gly (DFG) motif of the activation loop, with some, including FGFR1 kinase, appearing refractory to this so-called ‘DFG flip'. Recent inhibitor-bound structures have unexpectedly revealed FGFR1 for the first time in a ‘DFG-out' state. Here we use conformationally selective inhibitors as chemical probes for interrogation of the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our detailed structural and biophysical insights identify contributions from altered dynamics in distal elements, including the αH helix, towards the outstanding stability of the DFG-out complex with the inhibitor ponatinib. We conclude that the αC-β4 loop and ‘molecular brake' regions together impose a high energy barrier for this conformational rearrangement, and that this may have significance for maintaining autoinhibition in the non-phosphorylated basal state of FGFR1. PMID:26203596

  9. Structural delineation of stem-loop RNA binding by human TAF15 protein

    PubMed Central

    Kashyap, Maruthi; Ganguly, Akshay Kumar; Bhavesh, Neel Sarovar

    2015-01-01

    Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence. PMID:26612539

  10. Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase

    NASA Astrophysics Data System (ADS)

    Klein, Tobias; Vajpai, Navratna; Phillips, Jonathan J.; Davies, Gareth; Holdgate, Geoffrey A.; Phillips, Chris; Tucker, Julie A.; Norman, Richard A.; Scott, Andrew D.; Higazi, Daniel R.; Lowe, David; Thompson, Gary S.; Breeze, Alexander L.

    2015-07-01

    Protein tyrosine kinases differ widely in their propensity to undergo rearrangements of the N-terminal Asp-Phe-Gly (DFG) motif of the activation loop, with some, including FGFR1 kinase, appearing refractory to this so-called `DFG flip'. Recent inhibitor-bound structures have unexpectedly revealed FGFR1 for the first time in a `DFG-out' state. Here we use conformationally selective inhibitors as chemical probes for interrogation of the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our detailed structural and biophysical insights identify contributions from altered dynamics in distal elements, including the αH helix, towards the outstanding stability of the DFG-out complex with the inhibitor ponatinib. We conclude that the αC-β4 loop and `molecular brake' regions together impose a high energy barrier for this conformational rearrangement, and that this may have significance for maintaining autoinhibition in the non-phosphorylated basal state of FGFR1.

  11. Structural delineation of stem-loop RNA binding by human TAF15 protein.

    PubMed

    Kashyap, Maruthi; Ganguly, Akshay Kumar; Bhavesh, Neel Sarovar

    2015-11-27

    Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.

  12. Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation

    SciTech Connect

    Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Sobrado, Pablo; Tanner, John J.

    2012-11-01

    Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 {angstrom} movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k{sub cat}. Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.

  13. The LD loop as an important structural element required for transmission of the allosteric signal in the HtrA (DegP) protease from Escherichia coli.

    PubMed

    Figaj, Donata; Gieldon, Artur; Bartczak, Marlena; Koper, Tomasz; Zarzecka, Urszula; Lesner, Adam; Lipinska, Barbara; Skorko-Glonek, Joanna

    2016-09-01

    High-temperature requirement A (HtrA; DegP) from Escherichia coli, an important element of the extracytoplasmic protein quality-control system, is a member of the evolutionarily conserved family of serine proteases. The characteristic feature of this protein is its allosteric mode of activation. The regulatory loops, L3, L2, L1 and LD, play a crucial role in the transmission of the allosteric signal. Yet, the role of LD has not been fully elucidated. Therefore, we undertook a study to explain the role of the individual LD residues in inducing and maintaining the proteolytic activity of HtrA. We investigated the influence of amino acid substitutions located within the LD loop on the kinetics of a model substrate cleavage as well as on the dynamics of the oligomeric structure of HtrA. We found that the mutations that were expected to disturb the loop's structure and/or interactions with the remaining regulatory loops severely diminished the proteolytic activity of HtrA. The opposite effect, that is, increased activity, was observed for G174S substitution, which was predicted to strengthen the interactions mediated by LD. HtrAG174S protein had an equilibrium shifted toward the active enzyme and formed preferentially high-order oligomeric forms. PMID:27469236

  14. Structural loop between the cerebellum and the superior temporal sulcus: evidence from diffusion tensor imaging.

    PubMed

    Sokolov, Arseny A; Erb, Michael; Grodd, Wolfgang; Pavlova, Marina A

    2014-03-01

    The cerebellum is believed to play an essential role in a variety of motor and cognitive functions through reciprocal interaction with the cerebral cortex. Recent findings suggest that cerebellar involvement in the network specialized for visual body motion processing may be mediated through interaction with the right superior temporal sulcus (STS). Yet, the underlying pattern of structural connectivity between the STS and the cerebellum remains unidentified. In the present work, diffusion tensor imaging analysis on seeds derived from functional magnetic resonance imaging during a task on point-light biological motion perception uncovers a structural pathway between the right posterior STS and the left cerebellar lobule Crus I. The findings suggest existence of a structural loop underpinning bidirectional communication between the STS and cerebellum. This connection might also be of potential value for other visual social abilities. PMID:23169930

  15. Stationary vortex loops induced by filament interaction and local pinning in a chemical reaction-diffusion system.

    PubMed

    Jiménez, Zulma A; Steinbock, Oliver

    2012-08-31

    Scroll rings are three-dimensional excitation waves rotating around one-dimensional filament loops. In experiments with the Belousov-Zhabotinsky reaction we show that the collapse of these loops can be stopped by local pinning to only two unexcitable heterogeneities. The resulting vortices rotate around stationary but curved filaments. The absence of filament motion can be explained by repulsive interaction that counteracts the expected curvature-induced motion. The shape and key dependencies of the stationary filaments are well described by a curvature-flow model with additive interaction velocities that rapidly decrease with filament distance.

  16. Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity.

    PubMed

    Wongsurawat, Thidathip; Jenjaroenpun, Piroon; Kwoh, Chee Keong; Kuznetsov, Vladimir

    2012-01-01

    R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66,803 sequences defined by UCSC as 'known' genes. We found that ∼59% of these transcribed sequences contain at least one RLFS. We created R-loopDB (http://rloop.bii.a-star.edu.sg/), the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration and visualisation across a variety of bioinformatics sources. We found that many oncogenes and tumour suppressors (e.g. Tp53, BRCA1, BRCA2, Kras and Ptprd) and neurodegenerative diseases related genes (e.g. ATM, Park2, Ptprd and GLDC) could be prone to significant R-loop formation. Our findings suggest that R-loops provide a novel level of RNA-DNA interactome complexity, playing key roles in gene expression controls, mutagenesis, recombination process, chromosomal rearrangement, alternative splicing, DNA-editing and epigenetic modifications. RLFSs could be used as a novel source of prospective therapeutic targets.

  17. The one-loop matter bispectrum in the Effective Field Theory of Large Scale Structures

    DOE PAGESBeta

    Angulo, Raul E.; Foreman, Simon; Schmittfull, Marcel; Senatore, Leonardo

    2015-10-14

    With this study, given the importance of future large scale structure surveys for delivering new cosmological information, it is crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbative scheme to compute the clustering of dark matter in the weakly nonlinear regime in an expansion in k/kNL, where k is the wavenumber of interest and kNL is the wavenumber associated to the nonlinear scale. It has been recently shown that the EFTofLSS matches to 1% level the dark matter power spectrum at redshift zero up to k ≃ 0.3 hmore » Mpc–1 and k ≃ 0.6 h Mpc–1 at one and two loops respectively, using only one counterterm that is fit to data. Similar results have been obtained for the momentum power spectrum at one loop. This is a remarkable improvement with respect to former analytical techniques. Here we study the prediction for the equal-time dark matter bispectrum at one loop. We find that at this order it is sufficient to consider the same counterterm that was measured in the power spectrum. Without any remaining free parameter, and in a cosmology for which kNL is smaller than in the previously considered cases (σ8=0.9), we find that the prediction from the EFTofLSS agrees very well with N-body simulations up to k ≃ 0.25 h Mpc–1, given the accuracy of the measurements, which is of order a few percent at the highest k's of interest. While the fit is very good on average up to k ≃ 0.25 h Mpc–1, the fit performs slightly worse on equilateral configurations, in agreement with expectations that for a given maximum k, equilateral triangles are the most nonlinear.« less

  18. Structural Conservation Predominates Over Sequence Variability in the Crown of HIV Type 1's V3 Loop

    PubMed Central

    Almond, David; Kimura, Tetsuya; Kong, XiangPeng; Swetnam, James; Zolla-Pazner, Susan

    2010-01-01

    Abstract The diversity of HIV-1 is a confounding problem for vaccine design, as the human immune response appears to favor poor or strain-specific responses to any given HIV-1 virus strain. A significant portion of this diversity is manifested as sequence variability in the loops of HIV-1's surface envelope glycoprotein. Here we show that the most variable sequence positions in the third variable (V3) loop crown cluster to a small zone on the surface of one face of the V3 loop ß-hairpin conformation. These results provide a novel visualization of the gp120 V3 loop, specifically demonstrating a surprising preponderance of conserved three-dimensional structure in a highly sequence-variable region. From a structural point of view, there appears to be less diversity in this region of the HIV-1 “principle neutralizing domain” than previously appreciated. PMID:20560796

  19. Low-order design and high-order simulation of active closed-loop control for aerospace structures under construction

    NASA Technical Reports Server (NTRS)

    Balas, Mark J.

    1989-01-01

    Partially constructed/assembled structures in space are complicated enough but their dynamics will also be operating in closed-loop with feedback controllers. The dynamics of such structures are modeled by large-scale finite element models. The model dimension L is extremely large (approximately 10,000) while the numbers of actuators (M) and sensors (P) are small. The model parameters M(sub m) mass matrix, D(sub o) damping matrix, and K(sub o) stiffness matrix, are all symmetric and sparse (banded). Thus simulation of open-loop structure models of very large dimension can be accomplished by special integration techniques for sparse matrices. The problem of simulation of closed-loop control of such structures is complicated by the addition of controllers. Simulation of closed-loop controlled structures is an essential part of the controller design and evaluation process. Current research in the following areas is presented: high-order simulation of actively controlled aerospace structures; low-order controller design and SCI compensation for unmodeled dynamics; prediction of closed-loop stability using asymptotic eigenvalue series; and flexible robot manipulator control experiment.

  20. Loop Heat Pipe Temperature Oscillation Induced by Gravity Assist and Reservoir Heating

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Garrison, Matthew; Patel, Deepak; Robinson, Franklin; Ottenstein, Laura

    2015-01-01

    The Laser Thermal Control System (LCTS) for the Advanced Topographic Laser Altimeter System (ATLAS) to be installed on NASA's Ice, Cloud, and Land Elevation Satellite (ICESat-2) consists of a constant conductance heat pipe and a loop heat pipe (LHP) with an associated radiator. During the recent thermal vacuum testing of the LTCS where the LHP condenser/radiator was placed in a vertical position above the evaporator and reservoir, it was found that the LHP reservoir control heater power requirement was much higher than the analytical model had predicted. Even with the control heater turned on continuously at its full power, the reservoir could not be maintained at its desired set point temperature. An investigation of the LHP behaviors found that the root cause of the problem was fluid flow and reservoir temperature oscillations, which led to persistent alternate forward and reversed flow along the liquid line and an imbalance between the vapor mass flow rate in the vapor line and liquid mass flow rate in the liquid line. The flow and temperature oscillations were caused by an interaction between gravity and reservoir heating, and were exacerbated by the large thermal mass of the instrument simulator which modulated the net heat load to the evaporator, and the vertical radiator/condenser which induced a variable gravitational pressure head. Furthermore, causes and effects of the contributing factors to flow and temperature oscillations intermingled.

  1. Formation of large-scale structure from cosmic-string loops and cold dark matter

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Scherrer, Robert J.

    1987-01-01

    Some results from a numerical simulation of the formation of large-scale structure from cosmic-string loops are presented. It is found that even though G x mu is required to be lower than 2 x 10 to the -6th (where mu is the mass per unit length of the string) to give a low enough autocorrelation amplitude, there is excessive power on smaller scales, so that galaxies would be more dense than observed. The large-scale structure does not include a filamentary or connected appearance and shares with more conventional models based on Gaussian perturbations the lack of cluster-cluster correlation at the mean cluster separation scale as well as excessively small bulk velocities at these scales.

  2. Concerted loop motion triggers induced fit of FepA to ferric enterobactin.

    PubMed

    Smallwood, Chuck R; Jordan, Lorne; Trinh, Vy; Schuerch, Daniel W; Gala, Amparo; Hanson, Mathew; Hanson, Matthew; Shipelskiy, Yan; Majumdar, Aritri; Newton, Salete M C; Klebba, Phillip E

    2014-07-01

    Spectroscopic analyses of fluorophore-labeled Escherichia coli FepA described dynamic actions of its surface loops during binding and transport of ferric enterobactin (FeEnt). When FeEnt bound to fluoresceinated FepA, in living cells or outer membrane fragments, quenching of fluorophore emissions reflected conformational motion of the external vestibular loops. We reacted Cys sulfhydryls in seven surface loops (L2, L3, L4, L5, L7 L8, and L11) with fluorophore maleimides. The target residues had different accessibilities, and the labeled loops themselves showed variable extents of quenching and rates of motion during ligand binding. The vestibular loops closed around FeEnt in about a second, in the order L3 > L11 > L7 > L2 > L5 > L8 > L4. This sequence suggested that the loops bind the metal complex like the fingers of two hands closing on an object, by individually adsorbing to the iron chelate. Fluorescence from L3 followed a biphasic exponential decay as FeEnt bound, but fluorescence from all the other loops followed single exponential decay processes. After binding, the restoration of fluorescence intensity (from any of the labeled loops) mirrored cellular uptake that depleted FeEnt from solution. Fluorescence microscopic images also showed FeEnt transport, and demonstrated that ferric siderophore uptake uniformly occurs throughout outer membrane, including at the poles of the cells, despite the fact that TonB, its inner membrane transport partner, was not detectable at the poles.

  3. The temperature structure and pressure balance of magnetic loops in active regions. [in solar atmosphere

    NASA Technical Reports Server (NTRS)

    Foukal, P.

    1975-01-01

    EUV observations show many active region loops in lines formed at temperatures between 10,000 and 2,000,000 K. The brightest loops are associated with flux tubes leading to the umbrae of sunspots. It is shown that the high visibility of certain loops in transition region lines is due principally to a sharp radial decrease of temperature to chromospheric values toward the loop axis. The plasma density of these cool loops is not significantly greater than in the hot gas immediately surrounding it. Consequently, the internal gas pressure of the cool material is clearly lower. The hot material immediately surrounding the cool loops is generally denser than the external corona by a factor 3-4. When the active region is examined in coronal lines, this hot high pressure plasma shows up as loops that are generally parallel to the cool loops but significantly displaced laterally.

  4. ACL repair might induce further abnormality of gamma loop in the intact side of the quadriceps femoris.

    PubMed

    Konishi, Y U

    2011-04-01

    The purpose of this study was to investigate the effect of surgery on the gamma-loop in the quadriceps of patients with ACL injuries. We compared the response to vibration stimulation in subjects with ACL repair, subjects with ACL rupture, and normal subjects, by measuring the maximal strength and integrated electromyography (I-EMG) of the quadriceps. Pre-vibration data were obtained from each subject by measuring the MVC of the knee extension and the I-EMG from the vastus medialis, vastus lateralis, and rectus femoris. Vibration stimulation was applied to the infrapatellar tendon, followed immediately by repeating maximal strength and I-EMG recording. The results of this study indicated that alpha motor neuron activity of the intact side of the vastus lateralis in response to prolonged vibration stimulation was altered by surgery, but no effect was detected in the injured side. The results could suggest that abnormality of the gamma-loop existed even in the quadriceps of patients with ACL rupture since the vibration stimulus failed to elicit changes in ACL-rupture group as compared with those of normal subjects. In comparison, abnormality of the gamma-loop in the intact side of the QF was probably induced by the rupture, and further abnormality of gamma-loop was induced by surgery.

  5. Structure-based engineering of a minimal porin reveals loop-independent channel closure.

    PubMed

    Grosse, Wolfgang; Psakis, Georgios; Mertins, Barbara; Reiss, Philipp; Windisch, Dirk; Brademann, Felix; Bürck, Jochen; Ulrich, Anne; Koert, Ulrich; Essen, Lars-Oliver

    2014-07-29

    Porins, like outer membrane protein G (OmpG) of Escherichia coli, are ideal templates among ion channels for protein and chemical engineering because of their robustness and simple architecture. OmpG shows fast transitions between open and closed states, which were attributed to loop 6 (L6). As flickering limits single-channel-based applications, we pruned L6 by either 8 or 12 amino acids. While the open probabilities of both L6 variants resemble that of native OmpG, their gating frequencies were reduced by 63 and 81%, respectively. Using the 3.2 Å structure of the shorter L6 variant in the open state, we engineered a minimal porin (220 amino acids), where all remaining extramembranous loops were truncated. Unexpectedly, this minimized porin still exhibited gating, but it was 5-fold less frequent than in OmpG. The residual gating of the minimal pore is hence independent of L6 rearrangements and involves narrowing of the ion conductance pathway most probably driven by global stretching-flexing deformations of the membrane-embedded β-barrel.

  6. The integration of water loop heat pump and building structural thermal storage systems

    SciTech Connect

    Marseille, T.J.; Schliesing, J.S.

    1991-10-01

    Many commercial buildings need heat in one part and, at the same time, cooling in another part. Even more common is the need for heating during one part of the day and cooling during another in the same spaces. If that energy could be shifted or stored for later use, significant energy might be saved. If a building's heating and cooling subsystems could be integrated with the building's structural mass and used to collect, store, and deliver energy, the energy might be save cost-effectively. To explore this opportunity, researchers at the Pacific Northwest Laboratory (PNL) examined the thermal interactions between the heating, ventilating, and air-conditioning (HVAC) system and the structure of a commercial building. Computer models were developed to simulate the interactions in an existing building located in Seattle, Washington, to determine how these building subsystems could be integrated to improve energy efficiency. The HVAC subsystems in the existing building were modeled. These subsystems consist of decentralized water-source heat pumps (WSHP) in a closed water loop, connected to cooling towers for heat rejection during cooling mode and boilers to augment heating. An initial base case'' computer model of the Seattle building, as-built, was developed. Metered data available for the building were used to calibrate this model to ensure that the analysis would provide information that closely reflected the operation of a real building. The HVAC system and building structure were integrated in the model using the concrete floor slabs as thermal storage media. The slabs may be actively charged during off-peak periods with the chilled water in the loop and then either actively or passively discharged into the conditioned space during peak periods. 21 refs., 37 figs., 17 tabs.

  7. Two aspects of one loop structure: Unitarity delay in the Standard Model and modular invariance in string theory

    SciTech Connect

    Ahn, C.

    1989-08-01

    We study two aspects of one loop structures in quantum field theories which describe two different areas of particle physics: the one loop unitarity behavior of the Standard Model of electroweak interactions and modular invariance of string model theory. Loop expansion has its importance in that it contains quantum fluctuations due to all physical states in the theory. Therefore, by studying the various models to one loop, we can understand how the contents of the theory can contribute to physically measurable quantities and how the consistency at quantum level restricts the physical states of the theory, as well. In the first half of the thesis, we study one loop corrections to the process {ital e}{sup +}{ital e}{sup {minus}} {yields} {ital W}{sup +}{ital W}{sup {minus}}. In this process, there is a delicate unitarity-saving cancellation between s-channel and t-channel tree level Feynman diagrams. If the one loop contribution due to heavy particles corrects the channels asymmetrically, the cancellation, hence unitarity, will be delayed up to the mass scale of these heavy particles. We refer to this phenomena as the unitarity delay effect. Due to this effect, cross section below these mass scales can have significant radiative corrections which may provide an appropriate window through which we can see the high energy structure of the Standard Model from relatively low energy experiments. In the second half, we will show how quantum consistency can restrict the physical states in string theory. 53 refs., 13 figs.

  8. Properties and Modeling of Unresolved Fine Structure Loops Observed in the Solar Transition Region by IRIS

    NASA Astrophysics Data System (ADS)

    Brooks, David H.; Reep, Jeffrey W.; Warren, Harry P.

    2016-08-01

    Recent observations from the Interface Region Imaging Spectrograph (IRIS) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads. We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.

  9. Flow-Induced Axial Vascularization: The Arteriovenous Loop in Angiogenesis and Tissue Engineering.

    PubMed

    Leibig, Nico; Wietbrock, Johanna O; Bigdeli, Amir K; Horch, Raymund E; Kremer, Thomas; Kneser, Ulrich; Schmidt, Volker J

    2016-10-01

    Fabrication of a viable vascular network providing oxygen supply is identified as one crucial limiting factor to generate more complex three-dimensional constructs. The arteriovenous loop model provides initial blood supply and has a high angioinductive potency, making it suitable for vascularization of larger, tissue-engineered constructs. Also because of its angiogenic capabilities the arteriovenous loop is recently also used as a model to evaluate angiogenesis in vivo. This review summarizes the history of the arteriovenous loop model in research and its technical and surgical aspects. Through modifications of the isolation chamber and its containing matrices, tissue generation can be enhanced. In addition, matrices can be used as release systems for local application of growth factors, such as vascular endothelial growth factor and basic fibroblast growth factor, to affect vascular network formation. A special focus in this review is set on the assessment of angiogenesis in the arteriovenous loop model. This model provides good conditions for assessment of angiogenesis with the initial cell-free environment of the isolation chamber, which is vascularized by the arteriovenous loop. Because of the angiogenic capabilities of the arteriovenous loop model, different attempts were performed to create functional tissue in the isolation chamber for potential clinical application. Arteriovenous loops in combination with autologous bone marrow aspirate were already used to reconstruct large bone defects in humans. PMID:27673517

  10. Flow-Induced Axial Vascularization: The Arteriovenous Loop in Angiogenesis and Tissue Engineering.

    PubMed

    Leibig, Nico; Wietbrock, Johanna O; Bigdeli, Amir K; Horch, Raymund E; Kremer, Thomas; Kneser, Ulrich; Schmidt, Volker J

    2016-10-01

    Fabrication of a viable vascular network providing oxygen supply is identified as one crucial limiting factor to generate more complex three-dimensional constructs. The arteriovenous loop model provides initial blood supply and has a high angioinductive potency, making it suitable for vascularization of larger, tissue-engineered constructs. Also because of its angiogenic capabilities the arteriovenous loop is recently also used as a model to evaluate angiogenesis in vivo. This review summarizes the history of the arteriovenous loop model in research and its technical and surgical aspects. Through modifications of the isolation chamber and its containing matrices, tissue generation can be enhanced. In addition, matrices can be used as release systems for local application of growth factors, such as vascular endothelial growth factor and basic fibroblast growth factor, to affect vascular network formation. A special focus in this review is set on the assessment of angiogenesis in the arteriovenous loop model. This model provides good conditions for assessment of angiogenesis with the initial cell-free environment of the isolation chamber, which is vascularized by the arteriovenous loop. Because of the angiogenic capabilities of the arteriovenous loop model, different attempts were performed to create functional tissue in the isolation chamber for potential clinical application. Arteriovenous loops in combination with autologous bone marrow aspirate were already used to reconstruct large bone defects in humans.

  11. Quantifying the structure of the mesopelagic microbial loop from observed depth profiles of bacteria and protozoa

    NASA Astrophysics Data System (ADS)

    Tanaka, T.; Rassoulzadegan, F.; Thingstad, T. F.

    2004-08-01

    t is widely recognized that organic carbon exported to the ocean aphotic layer is significantly consumed by heterotrophic organisms such as bacteria and zooplankton in the mesopelagic layer. However, very little is known for the trophic link between bacteria and zooplankton or the structure of the microbial loop in this layer. In the northwestern Mediterranean, recent studies have shown that viruses, bacteria, heterotrophic nanoflagellates, and ciliates distribute down to 2000 m with group-specific depth-dependent decreases, and that bacterial production decreases with depth down to 1000 m. Here we show that such data can be analyzed using a simple steady-state food chain model to quantify the carbon flow from bacteria to zooplankton over the mesopelagic layer. The model indicates that a similar amount of bacterial production is allocated to viruses and heterotrophic nanoflagellates, and that heterotrophic nanoflagellates are the important remineralizers.

  12. The one-loop matter bispectrum in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul E.; Foreman, Simon; Schmittfull, Marcel; Senatore, Leonardo

    2015-10-14

    With this study, given the importance of future large scale structure surveys for delivering new cosmological information, it is crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbative scheme to compute the clustering of dark matter in the weakly nonlinear regime in an expansion in k/kNL, where k is the wavenumber of interest and kNL is the wavenumber associated to the nonlinear scale. It has been recently shown that the EFTofLSS matches to 1% level the dark matter power spectrum at redshift zero up to k ≃ 0.3 h Mpc–1 and k ≃ 0.6 h Mpc–1 at one and two loops respectively, using only one counterterm that is fit to data. Similar results have been obtained for the momentum power spectrum at one loop. This is a remarkable improvement with respect to former analytical techniques. Here we study the prediction for the equal-time dark matter bispectrum at one loop. We find that at this order it is sufficient to consider the same counterterm that was measured in the power spectrum. Without any remaining free parameter, and in a cosmology for which kNL is smaller than in the previously considered cases (σ8=0.9), we find that the prediction from the EFTofLSS agrees very well with N-body simulations up to k ≃ 0.25 h Mpc–1, given the accuracy of the measurements, which is of order a few percent at the highest k's of interest. While the fit is very good on average up to k ≃ 0.25 h Mpc–1, the fit performs slightly worse on equilateral configurations, in agreement with expectations that for a given maximum k, equilateral triangles are the most nonlinear.

  13. Amplification activation loop between caspase-8 and -9 dominates artemisinin-induced apoptosis of ASTC-a-1 cells.

    PubMed

    Xiao, Fenglian; Gao, Weijie; Wang, Xiaoping; Chen, Tongsheng

    2012-06-01

    Although caspases have been demonstrated to be involved in artemisinin (ARTE)-induced apoptosis, their exact functions are not well understood. The aim of this report is to explore the roles of caspase-8, -9 and -3 during ARTE-induced apoptosis in human lung adenocarcinoma (ASTC-a-1) cells. ARTE treatment induces a rapid generation of reactive oxygen species (ROS), and ROS-dependent apoptosis as well as the activation of caspase-8, -9 and -3 via time- and dose-dependent fashion. Of upmost importance, inhibition of caspase-8 or -9, but not caspase-3, almost completely blocks the ARTE-induced not only activation of the caspase-8, -9 and -3 but also apoptosis. In addition, the apoptotic process triggered by ARTE does not involve the Bid cleavage, tBid translocation, significant loss of mitochondrial membrane potential and cytochrome c release from mitochondria. Moreover, silencing Bax/Bak does not prevent the ATRE-induced cell death as well as the activation of caspase-8, -9 and -3. Collectively, our data firstly demonstrate that ARTE triggers a ROS-mediated positive feedback amplification activation loop between caspase-8 and -9 independent of mitochondria, which dominantly mediated the ARTE-induced apoptosis via a caspase-3-independent apoptotic pathway in ASTC-a-1 cells. Our findings imply a potential to develop new derivatives from artemisinin to effectively initiate the amplification activation loop of caspases. PMID:22434375

  14. Amplification activation loop between caspase-8 and -9 dominates artemisinin-induced apoptosis of ASTC-a-1 cells.

    PubMed

    Xiao, Fenglian; Gao, Weijie; Wang, Xiaoping; Chen, Tongsheng

    2012-06-01

    Although caspases have been demonstrated to be involved in artemisinin (ARTE)-induced apoptosis, their exact functions are not well understood. The aim of this report is to explore the roles of caspase-8, -9 and -3 during ARTE-induced apoptosis in human lung adenocarcinoma (ASTC-a-1) cells. ARTE treatment induces a rapid generation of reactive oxygen species (ROS), and ROS-dependent apoptosis as well as the activation of caspase-8, -9 and -3 via time- and dose-dependent fashion. Of upmost importance, inhibition of caspase-8 or -9, but not caspase-3, almost completely blocks the ARTE-induced not only activation of the caspase-8, -9 and -3 but also apoptosis. In addition, the apoptotic process triggered by ARTE does not involve the Bid cleavage, tBid translocation, significant loss of mitochondrial membrane potential and cytochrome c release from mitochondria. Moreover, silencing Bax/Bak does not prevent the ATRE-induced cell death as well as the activation of caspase-8, -9 and -3. Collectively, our data firstly demonstrate that ARTE triggers a ROS-mediated positive feedback amplification activation loop between caspase-8 and -9 independent of mitochondria, which dominantly mediated the ARTE-induced apoptosis via a caspase-3-independent apoptotic pathway in ASTC-a-1 cells. Our findings imply a potential to develop new derivatives from artemisinin to effectively initiate the amplification activation loop of caspases.

  15. Concerted loop motion triggers induced fit of FepA to ferric enterobactin

    PubMed Central

    Smallwood, Chuck R.; Jordan, Lorne; Trinh, Vy; Schuerch, Daniel W.; Gala, Amparo; Hanson, Mathew; Shipelskiy, Yan; Majumdar, Aritri; Newton, Salete M.C.

    2014-01-01

    Spectroscopic analyses of fluorophore-labeled Escherichia coli FepA described dynamic actions of its surface loops during binding and transport of ferric enterobactin (FeEnt). When FeEnt bound to fluoresceinated FepA, in living cells or outer membrane fragments, quenching of fluorophore emissions reflected conformational motion of the external vestibular loops. We reacted Cys sulfhydryls in seven surface loops (L2, L3, L4, L5, L7 L8, and L11) with fluorophore maleimides. The target residues had different accessibilities, and the labeled loops themselves showed variable extents of quenching and rates of motion during ligand binding. The vestibular loops closed around FeEnt in about a second, in the order L3 > L11 > L7 > L2 > L5 > L8 > L4. This sequence suggested that the loops bind the metal complex like the fingers of two hands closing on an object, by individually adsorbing to the iron chelate. Fluorescence from L3 followed a biphasic exponential decay as FeEnt bound, but fluorescence from all the other loops followed single exponential decay processes. After binding, the restoration of fluorescence intensity (from any of the labeled loops) mirrored cellular uptake that depleted FeEnt from solution. Fluorescence microscopic images also showed FeEnt transport, and demonstrated that ferric siderophore uptake uniformly occurs throughout outer membrane, including at the poles of the cells, despite the fact that TonB, its inner membrane transport partner, was not detectable at the poles. PMID:24981231

  16. [Loop organization of eukaryotic chromosomes and triple-stranded DNA structures].

    PubMed

    Glazkov, M V

    2011-01-01

    To study possible involvement of polypurine and polypyrimidine DNA tracks potentially capable to form triple-stranded structures (H-form of DNA) in compactization of eukaryotic chromosomes a search in silico for "complementary" polypurine and polypyrimidine tracks within 12 eukaryotic gene nucleotide sequences was carried out. Polypurine and polypyrimidine tracks (10-11 b.p.) potentially capable of interacting with each other with the formation of triplex structures ("structurizing" regions) has been shown to be located in chromosomal locus of genes, predominantly in introns and flanking regions. In the case of in vivo realization of such DNA-DNA interactions the chromosomal gene domains can be folded into several small loops. An involvement of DNA triplexes in the chromosomal gene loci compactization may be associated with the gene functioning. The analogous analysis carried out for nucleotide sequences of long (LINE) and short (SINE) repeats dispersed over the genome as well as of satellite DNA has demonstrated a fundamental identity between mechanisms of chromosomal encoding and non-coding regions' compactization.

  17. Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms

    PubMed Central

    Balasco, Nicole; Esposito, Luciana; Simone, Alfonso De; Vitagliano, Luigi

    2013-01-01

    It has been recently discovered that the connection of secondary structure elements (ββ-unit, βα- and αβ-units) in proteins follows quite stringent principles regarding the chirality and the orientation of the structural units (Koga et al., Nature 2012;491:222–227). By exploiting these rules, a number of protein scaffolds endowed with a remarkable thermal stability have been designed (Koga et al., Nature 2012;491:222–227). By using structural databases of proteins isolated from either mesophilic or thermophilic organisms, we here investigate the influence of supersecondary associations on the thermal stability of natural proteins. Our results suggest that β-hairpins of proteins from thermophilic organisms are very frequently characterized by shortenings of the loops. Interestingly, this shortening leads to states that display a very strong preference for the most common connectivity of the strands observed in native protein hairpins. The abundance of selective states in these proteins suggests that they may achieve a high stability by adopting a strategy aimed to reduce the possible conformations of the unfolded ensemble. In this scenario, our data indicate that the shortening is effective if it increases the adherence to these rules. We also show that this mechanism may operate in the stabilization of well-known protein folds (thioredoxin and RNase A). These findings suggest that future investigations aimed at defining mechanism of protein stabilization should also consider these effects. PMID:23661276

  18. Crystal structure of baculovirus P35: role of a novel reactive site loop in apoptotic caspase inhibition.

    PubMed Central

    Fisher, A J; Cruz, W d; Zoog, S J; Schneider, C L; Friesen, P D

    1999-01-01

    The aspartate-specific caspases are critical protease effectors of programmed cell death and consequently represent important targets for apoptotic intervention. Baculovirus P35 is a potent substrate inhibitor of metazoan caspases, a property that accounts for its unique effectiveness in preventing apoptosis in phylogenetically diverse organisms. Here we report the 2.2 A resolution crystal structure of P35, the first structure of a protein inhibitor of the death caspases. The P35 monomer possesses a solvent-exposed loop that projects from the protein's main beta-sheet core and positions the requisite aspartate cleavage site at the loop's apex. Distortion or destabilization of this reactive site loop by site-directed mutagenesis converted P35 to an efficient substrate which, unlike wild-type P35, failed to interact stably with the target caspase or block protease activity. Thus, cleavage alone is insufficient for caspase inhibition. These data are consistent with a new model wherein the P35 reactive site loop participates in a unique multi-step mechanism in which the spatial orientation of the loop with respect to the P35 core determines post-cleavage association and stoichiometric inhibition of target caspases. PMID:10205157

  19. Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding

    SciTech Connect

    De Ioannes, Pablo; Escalante, Carlos R.; Aggarwal, Aneel K.

    2013-11-20

    Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-{beta} (IFN-{beta}) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray structures of IRF-3 and IRF-7 DNA binding domains (DBDs) bound to IFN-{beta} promoter elements revealed flexibility in the loops (L1-L3) and the residues that make contacts with the target sequence. To characterize the conformational changes that occur on DNA binding and how they differ between IRF family members, we have solved the X-ray structures of IRF-3 and IRF-7 DBDs in the absence of DNA. We found that loop L1, carrying the conserved histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered in apo IRF-7. This is reflected in differences in DNA binding affinities when the conserved histidine in loop L1 is mutated to alanine in the two proteins. The stability of loop L1 in IRF-7 derives from a unique combination of hydrophobic residues that pack against the protein core. Together, our data show that differences in flexibility of loop L1 are an important determinant of differential IRF-DNA binding.

  20. Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

    PubMed Central

    Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

    2010-01-01

    SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

  1. Structural Insights Into Substrate Recognition by the Neurospora Varkud Satellite Ribozyme: Importance of U-Turns at the Kissing-Loop Junction

    PubMed Central

    2013-01-01

    Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson–Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson–Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson–Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme. PMID:24325625

  2. Immobilized stem-loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA.

    PubMed

    Bockisch, Benjamin; Grunwald, Thomas; Spillner, Edzard; Bredehorst, Reinhard

    2005-01-01

    We have designed and evaluated novel DNA stem-loop structured probes for enzymatic detection of nucleic acid targets. These probes constitute a novel class of conformational switches for enzymatic activity, which in the absence of a target sterically shield an affinity label and upon hybridization of the target to the recognition sequence that forms the loop of the probe restore accessibility of the label for the binding of a reporter enzyme. Analysis of probe characteristics revealed stem stability as the most important parameter governing detection functionality, while other factors such as the length of linker molecules attaching the label to the stem-loop structure and the nature of the solid support proved to be less critical. Apparently, the bulky nature of the reporter enzyme facilitates shielding of the label in the absence of the target, thereby conferring considerable structural tolerance to the conformational switch system. The stem-loop structured probes allow sensitive detection of unlabeled nucleic acid targets. Employing a microtiter assay format, 4 ng of bacterial 16S ribosomal RNA corresponding to 8 fmol could be detected, which can be compared favorably with current immobilized molecular beacon concepts based on fluorescence detection.

  3. Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study.

    PubMed

    Lim, Kah Wai; Jenjaroenpun, Piroon; Low, Zhen Jie; Khong, Zi Jian; Ng, Yi Siang; Kuznetsov, Vladimir Andreevich; Phan, Anh Tuân

    2015-06-23

    Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters. Our analysis suggested that these should cover close to half of total SLQS in the entire genome. Among these, 48 508 SLQS were strand-specifically located in genic/promoter regions, with the majority of genes displaying a low number of SLQS. Notably, genes containing abundant SLQS clusters were strongly associated with brain tissues. Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. In vitro formation of diverse QDH by selective SLQS hits were successfully verified by nuclear magnetic resonance spectroscopy. Folding topologies of two SLQS were elucidated in detail. We also demonstrated that sequence changes at mutation/single-nucleotide polymorphism loci could affect the structural conformations adopted by SLQS. Thus, our predicted SLQS offer novel insights into the potential involvement of QDH in diverse (patho)biological processes and could represent novel regulatory signals.

  4. Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study

    PubMed Central

    Lim, Kah Wai; Jenjaroenpun, Piroon; Low, Zhen Jie; Khong, Zi Jian; Ng, Yi Siang; Kuznetsov, Vladimir Andreevich; Phan, Anh Tuân

    2015-01-01

    Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex–duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters. Our analysis suggested that these should cover close to half of total SLQS in the entire genome. Among these, 48 508 SLQS were strand-specifically located in genic/promoter regions, with the majority of genes displaying a low number of SLQS. Notably, genes containing abundant SLQS clusters were strongly associated with brain tissues. Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. In vitro formation of diverse QDH by selective SLQS hits were successfully verified by nuclear magnetic resonance spectroscopy. Folding topologies of two SLQS were elucidated in detail. We also demonstrated that sequence changes at mutation/single-nucleotide polymorphism loci could affect the structural conformations adopted by SLQS. Thus, our predicted SLQS offer novel insights into the potential involvement of QDH in diverse (patho)biological processes and could represent novel regulatory signals. PMID:25958397

  5. Protein kinase–inhibitor database: Structural variability of and inhibitor interactions with the protein kinase P-loop

    PubMed Central

    Patel, Ronak Y.; Doerksen, Robert J.

    2011-01-01

    Structure based drug design of protein-kinase inhibitors has been facilitated by availability of an enormous number of structures in the Protein Databank (PDB), systematic analyses of which can provide insight into the factors which govern ligand–protein kinase interactions and into the conformational variability of the protein kinases. In this study, a non-redundant database containing 755 unique, curated and annotated PDB protein kinase–inhibitor complexes (each consisting of a single protein kinase chain, a ligand and water molecules around the ligand) was created. With this dataset, analyses were performed of protein conformational variability and interactions of ligands with 11 P-loop residues. Analysis of ligand–protein interactions included ligand atom preference, ligand–protein hydrogen bonds and the number and position of crystallographic water molecules around important P-loop residues. Analysis of variability in the conformation of the P-loop considered backbone and side-chain dihedral angles, and solvent accessible surface area (SASA). A distorted conformation of the P-loop was observed for some of the protein kinase structures. Lower SASA was observed for the hydrophobic residue in β1 of several members of the AGC family of protein kinases. Our systematic studies were performed amino-acid by amino-acid, which is unusual for analyses of protein kinase–inhibitor complexes. PMID:20681595

  6. Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

    PubMed Central

    Chu, V.; Freitag, S.; Le Trong, I.; Stenkamp, R. E.; Stayton, P. S.

    1998-01-01

    A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin. PMID:9568892

  7. Initial findings: The integration of water loop heat pump and building structural thermal storage systems

    SciTech Connect

    Marseille, T.J.; Johnson, B.K.; Wallin, R.P.; Chiu, S.A.; Crawley, D.B.

    1989-01-01

    This report is one in a series of reports describing research activities in support of the US Department of Energy (DOE) Commercial Building System Integration Research Program. The goal of the program is to develop the scientific and technical basis for improving integrated decision-making during design and construction. Improved decision-making could significantly reduce buildings' energy use by the year 2010. The objectives of the Commercial Building System Integration Research Program are: to identify and quantify the most significant energy-related interactions among building subsystems; to develop the scientific and technical basis for improving energy related interactions in building subsystems; and to provide guidance to designers, owners, and builders for improving the integration of building subsystems for energy efficiency. The lead laboratory for this program is the Pacific Northwest Laboratory. A wide variety of expertise and resources from industry, academia, other government entities, and other DOE laboratories are used in planning, reviewing and conducting research activities. Cooperative and complementary research, development, and technology transfer activities with other interested organizations are actively pursued. In this report, the interactions of a water loop heat pump system and building structural mass and their effect on whole-building energy performance is analyzed. 10 refs., 54 figs., 1 tab.

  8. Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops

    NASA Astrophysics Data System (ADS)

    Pugnaloni, Luis A.; Carlevaro, C. Manuel; Kramár, M.; Mischaikow, K.; Kondic, L.

    2016-06-01

    The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016), 10.1103/PhysRevE.93.062903], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network's topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants.

  9. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    NASA Astrophysics Data System (ADS)

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-01

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  10. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.

    PubMed

    Wang, Beibei; Predeus, Alexander V; Burton, Zachary F; Feig, Michael

    2013-08-01

    An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.

  11. Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops.

    PubMed

    Pugnaloni, Luis A; Carlevaro, C Manuel; Kramár, M; Mischaikow, K; Kondic, L

    2016-06-01

    The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016)10.1103/PhysRevE.93.062903], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network's topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants. PMID:27415342

  12. Structural mimicry of a-loop tyrosine phosphorylation by a pathogenic FGF receptor 3 mutation.

    PubMed

    Huang, Zhifeng; Chen, Huaibin; Blais, Steven; Neubert, Thomas A; Li, Xiaokun; Mohammadi, Moosa

    2013-10-01

    The K650E gain-of-function mutation in the tyrosine kinase domain of FGF receptor 3 (FGFR3) causes Thanatophoric Dysplasia type II, a neonatal lethal congenital dwarfism syndrome, and when acquired somatically, it contributes to carcinogenesis. In this report, we determine the crystal structure of the FGFR3 kinase domain harboring this pathogenic mutation and show that the mutation introduces a network of intramolecular hydrogen bonds to stabilize the active-state conformation. In the crystal, the mutant FGFR3 kinases are caught in the act of trans-phosphorylation on a kinase insert autophosphorylation site, emphasizing the fact that the K650E mutation circumvents the requirement for A-loop tyrosine phosphorylation in kinase activation. Analysis of this trans-phosphorylation complex sheds light onto the determinants of tyrosine trans-phosphorylation specificity. We propose that the targeted inhibition of this pathogenic FGFR3 kinase may be achievable by small molecule kinase inhibitors that selectively bind the active-state conformation of FGFR3 kinase.

  13. Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops.

    PubMed

    Pugnaloni, Luis A; Carlevaro, C Manuel; Kramár, M; Mischaikow, K; Kondic, L

    2016-06-01

    The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016)10.1103/PhysRevE.93.062903], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network's topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants.

  14. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    SciTech Connect

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-15

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  15. Statistical characterization of the internal structure of noiselike pulses using a nonlinear optical loop mirror

    NASA Astrophysics Data System (ADS)

    Pottiez, O.; Paez-Aguirre, R.; Cruz, J. L.; Andrés, M. V.; Kuzin, E. A.

    2016-10-01

    In this work we study statistically the internal structure of noiselike pulses generated by a passively mode-locked fiber laser. For this purpose, we use a technique that allows estimating the distribution of the amplitudes of the sub-pulses in the bunch. The technique takes advantage of the fast response of the optical Kerr effect in a fiber nonlinear optical loop mirror (NOLM). It requires the measurement of the energy transfer characteristic of the pulses through the NOLM, and the numerical resolution of a system of nonlinear algebraic equations. The results yield a strongly asymmetric distribution, with a high-amplitude tail that is compatible with the existence of extreme-intensity sub-pulses in the bunch. Following the recent discovery of pulse-energy rogue waves and spectral rogue waves in the noiselike pulse regime, we propose a new way to look for extreme events in this particular mode of operation of mode-locked fiber lasers, and confirm that rogue wave generation is a key ingredient in the complex dynamics of these unconventional pulses.

  16. Characterization of strain-induced martensite phase in austenitic stainless steel using a magnetic minor-loop scaling relation

    SciTech Connect

    Kobayashi, Satoru; Saito, Atsushi; Takahashi, Seiki; Kamada, Yasuhiro; Kikuchi, Hiroaki

    2008-05-05

    We propose a combined magnetic method using a scaling power-law rule and initial permeability in magnetic minor hysteresis loops for characterization of ferromagnetic {alpha}{sup '} martensites in austenitic stainless steel. The scaling power law between the hysteresis loss and remanence is universal, being independent of volume fraction of strain-induced {alpha}{sup '} martensites. A coefficient of the power law largely decreases with volume fraction, while the initial permeability linearly increases, reflecting a change in the morphology and quantity of martensites, respectively. The present method is highly effective for integrity assessment of austenitic stainless steels because of the sensitivity and extremely low measurement field.

  17. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction.

    PubMed

    Oliva, B; Bates, P A; Querol, E; Avilés, F X; Sternberg, M J

    1998-06-26

    A computer-based algorithm was used to cluster the loops forming the complementarity determining region (CDR) 3 of the heavy chain (H3) into canonical classes. Previous analyses of the three-dimensional structures of CDR loops (also known as the hypervariable regions) within antibody immunoglobulin variable domains have shown that for five of the six CDRs there are only a few main-chain conformations (known as canonical forms) that show clear relationships between sequence and structure. However, the larger variation in length and conformation of loops within H3 has limited the classification of these loops into canonical forms. The clustering procedure presented here is based on aligning the Ramachandran-coded main-chain conformation of the residues using a dynamic algorithm that allows the insertion of gaps to obtain an optimum alignment. A total of 41 H3 loops out of 62 non-identical loops, extracted from the Brookhaven Protein Data Bank, have been automatically grouped into 22 clusters. Inspection of the clusters for consensus sequences or intra-loop interactions or invariant conformation led to the proposal of 13 canonical forms representing 31 loops. These canonical forms include a consideration of the geometry of both the take-off region adjacent to the bracing beta-strands and the remaining loop apex. Subsequently a new set of 15 H3 loops not included in the initial analysis was considered. The clustering procedure was repeated and nine of these 15 loops could be assigned to original clusters, including seven to canonical forms. A sequence profile was generated for each canonical form from the original set of loops and matched against the sequences of the new H3 loops. For five out of the seven new H3 loops that were in a canonical form, the correct form was identified at first rank by this predictive scheme. PMID:9642095

  18. Regulative Loops, Step Loops and Task Loops

    ERIC Educational Resources Information Center

    VanLehn, Kurt

    2016-01-01

    This commentary suggests a generalization of the conception of the behavior of tutoring systems, which the target article characterized as having an outer loop that was executed once per task and an inner loop that was executed once per step of the task. A more general conception sees these two loops as instances of regulative loops, which…

  19. Structure-function relationships of curaremimetic neurotoxin loop 2 and of a structurally similar segment of rabies virus glycoprotein in their interaction with the nicotinic acetylcholine receptor

    SciTech Connect

    Lentz, T.L. )

    1991-11-12

    Peptides corresponding to portions of curaremimetic neurotoxin loop 2 and to a structurally similar segment of rabies virus glycoprotein were synthetically modified in order to gain information on structure-function relationships of neurotoxin loop 2 interactions with the acetylcholine receptor. Binding of synthetic peptides to the acetylcholine receptor of Torpedo electric organ membranes was assessed by measuring their ability to inhibit the binding of {sup 125}I-{alpha}-bungarotoxin to the receptor. The peptides showing the highest affinity for the receptor were a peptide corresponding to the sequence of loop 2 (residues 25-44) of Ophiophagus hannah (king cobra) toxin b and the structurally similar segment of CVS rabies virus glycoprotein. These affinities were comparable to those of d-tubocurarine and suberyldicholine. These results demonstrate the importance of loop 2 in the neurotoxin interaction with the receptor. N- and C-terminal deletions of the loop 2 peptides and substitution of residues invariant or highly conserved among neurotoxins were performed in order to determine the role of individual residues in binding. Residues 25-40 are the most crucial in the interaction with the acetylcholine receptor. Since this region of the glycoprotein contains residues corresponding to all of the functionally invariant neurotoxin residues, it may interact with the acetylcholine receptor through a mechanism similar to that of the neurotoxins.

  20. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    SciTech Connect

    Kang, C.H.; Lockshin, C.; Rich, A.

    1995-04-25

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-{angstrom} resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C-C{sup +} hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5{prime} thymine Hoogsteen-base-paired to the third adenine. The 5{prime} end of this loop is in close proximity to the 3{prime} end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands. 25 refs., 5 figs.

  1. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    NASA Technical Reports Server (NTRS)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  2. Structural basis of conformational transitions in the active site and 80′s loop in the FK506-binding protein FKBP12

    PubMed Central

    Mustafi, Sourajit M.; Brecher, Matthew; Zhang, Jing; Li, Hongmin; Lemaster, David M.; Hernández, Griselda

    2014-01-01

    The extensive set of NMR doublings exhibited by the immunophilin FKBP12 (FK506-binding protein 12) arose from a slow transition to the cis-peptide configuration at Gly89 near the tip of the 80′s loop, the site for numerous protein-recognition interactions for both FKBP12 and other FKBP domain proteins. The 80′s loop also exhibited linebroadening, indicative of microsecond to millisecond conformational dynamics, but only in the trans-peptide state. The G89A variant shifted the trans–cis peptide equilibrium from 88:12 to 33:67, whereas a proline residue substitution induced fully the cis-peptide configuration. The 80′s loop conformation in the G89P crystal structure at 1.50 Å resolution differed from wild-type FKBP12 primarily at residues 88, 89 and 90, and it closely resembled that reported for FKBP52. Structure-based chemical-shift predictions indicated that the microsecond to millisecond dynamics in the 80′s loop probably arose from a concerted main chain (ψ88 and ϕ89) torsion angle transition. The indole side chain of Trp59 at the base of the active-site cleft was reoriented ~90o and the adjacent backbone was shifted in the G89P crystal structure. NOE analysis of wild-type FKBP12 demonstrated that this indole populates the perpendicular orientation at 20%. The 15N relaxation analysis was consistent with the indole reorientation occurring in the nanosecond timeframe. Recollection of the G89P crystal data at 1.20 Å resolution revealed a weaker wild-type-like orientation for the indole ring. Differences in the residues that underlie the Trp59 indole ring and altered interactions linking the 50′s loop to the active site suggested that reorientation of this ring may be disfavoured in the other six members of the FKBP domain family that bear this active-site tryptophan residue. PMID:24405377

  3. Cation-induced stabilization of the engineered cation-binding loop in cytochrome c peroxidase (CcP).

    PubMed

    Bhaskar, B; Bonagura, Christopher A; Li, Huiying; Poulos, Thomas L

    2002-02-26

    We have previously shown that the K(+) site found in the proximal heme pocket of ascorbate peroxidase (APX) could be successfully engineered into the closely homologous cytochrome c peroxidase (CcP) [Bonagura et al., (1996) Biochemistry 35, 6107-6115; Bonagura et al. (1999) Biochemistry 38, 5538-5545]. In addition, specificity could be switched to binding Ca(2+) as found in other peroxidases [Bonagura et al. (1999) J. Biol. Chem. 274, 37827-37833]. The introduction of a proximal cation-binding site also promotes conversion of the Trp191 containing cation-binding loop from a "closed" to an "open" conformer. In the present study we have changed a crucial hinge residue of the cation-binding loop, Asn195, to Pro which stabilizes the loop, albeit, only in the presence of bound K(+). The crystal structure of this mutant, N195PK2, has been refined to 1.9 A. As predicted, introduction of this crucial hinge residue stabilizes the cation-binding loop in the presence of the bound K(+). As in earlier work, the characteristic EPR signal of Trp191 cation radical becomes progressively weaker with increasing [K(+)] and the lifetime of the Trp191 radical also has been considerably shortened in this mutant. This mutant CcP exhibits reduced enzyme activity, which could be titrated to lower levels with increasing [K(+)] when horse heart cytochrome c is the substrate. However, with yeast cytochrome c as the substrate, the mutant was as active as wild-type at low ionic strength, but 40-fold lower at high ionic strength. We attribute this difference to a change in the rate-limiting step as a function of ionic strength when yeast cytochrome c is the substrate. PMID:11851415

  4. Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease

    PubMed Central

    Zühlsdorf, Martin; Werten, Sebastiaan; Klupp, Barbara G.; Palm, Gottfried J.; Mettenleiter, Thomas C.; Hinrichs, Winfried

    2015-01-01

    Herpesviruses encode a characteristic serine protease with a unique fold and an active site that comprises the unusual triad Ser-His-His. The protease is essential for viral replication and as such constitutes a promising drug target. In solution, a dynamic equilibrium exists between an inactive monomeric and an active dimeric form of the enzyme, which is believed to play a key regulatory role in the orchestration of proteolysis and capsid assembly. Currently available crystal structures of herpesvirus proteases correspond either to the dimeric state or to complexes with peptide mimetics that alter the dimerization interface. In contrast, the structure of the native monomeric state has remained elusive. Here, we present the three-dimensional structures of native monomeric, active dimeric, and diisopropyl fluorophosphate-inhibited dimeric protease derived from pseudorabies virus, an alphaherpesvirus of swine. These structures, solved by X-ray crystallography to respective resolutions of 2.05, 2.10 and 2.03 Å, allow a direct comparison of the main conformational states of the protease. In the dimeric form, a functional oxyanion hole is formed by a loop of 10 amino-acid residues encompassing two consecutive arginine residues (Arg136 and Arg137); both are strictly conserved throughout the herpesviruses. In the monomeric form, the top of the loop is shifted by approximately 11 Å, resulting in a complete disruption of the oxyanion hole and loss of activity. The dimerization-induced allosteric changes described here form the physical basis for the concentration-dependent activation of the protease, which is essential for proper virus replication. Small-angle X-ray scattering experiments confirmed a concentration-dependent equilibrium of monomeric and dimeric protease in solution. PMID:26161660

  5. Effective field theory of large scale structure at two loops: The apparent scale dependence of the speed of sound

    NASA Astrophysics Data System (ADS)

    Baldauf, Tobias; Mercolli, Lorenzo; Zaldarriaga, Matias

    2015-12-01

    We study the effective field theory (EFT) of large-scale structure for cosmic density and momentum fields. We show that the finite part of the two-loop calculation and its counterterms introduces an apparent scale dependence for the leading-order parameter cs2 of the EFT starting at k =0.1 h Mpc-1 . These terms limit the range over which one can trust the one-loop EFT calculation at the 1% level to k <0.1 h Mpc-1 at redshift z =0 . We construct a well-motivated one-parameter ansatz to fix the relative size of the one- and two-loop counterterms using their high-k sensitivity. Although this one-parameter model is a very restrictive choice for the counterterms, it explains the apparent scale dependence of cs2 seen in simulations. It is also able to capture the scale dependence of the density power spectrum up to k ≈0.3 h Mpc-1 at the 1% level at redshift z =0 . Considering a simple scheme for the resummation of large-scale motions, we find that the two-loop calculation reduces the need for this IR resummation at k <0.2 h Mpc-1 . Finally, we extend our calculation to momentum statistics and show that the same one-parameter model can also describe density-momentum and momentum-momentum statistics.

  6. Correlating STM Contrast and Atomic-Scale Structure by Chemical Modification: Vacancy Dislocation Loops on FeO/Pt(111)

    SciTech Connect

    Merte, L. R.; Knudsen, Jan; Grabow, Lars C.; Vang, Ronnie T.; Laegsgaard, E.; Mavrikakis, Manos; Besenbacher, Fleming

    2008-11-28

    By chemically modifying the FeO(111) thin film on Pt(111), we show that it is possible to unambiguously correlate its STM morphology with its underlying structure without recourse to STM simulations. Partial reduction of the oxide surface leads to the formation of triangularly-shaped oxygen vacancy dislocation loops at specific sites in the moiré structure of the film. Their presence allows unambiguous identification of the high-symmetry domains of the moiré structure, whose differing chemical properties govern the templating effect on adsorbed metal atoms, clusters and molecules.

  7. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

    SciTech Connect

    Mortenson, David E.; Kreitler, Dale F.; Yun, Hyun Gi; Gellman, Samuel H. Forest, Katrina T.

    2013-12-01

    Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure. The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of β-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the l- and d-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a d,l mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.

  8. The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop.

    PubMed Central

    Bénas, P; Bec, G; Keith, G; Marquet, R; Ehresmann, C; Ehresmann, B; Dumas, P

    2000-01-01

    We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon. PMID:11073212

  9. An explanation of one-loop induced h → μτ decay

    NASA Astrophysics Data System (ADS)

    Baek, Seungwon; Nomura, Takaaki; Okada, Hiroshi

    2016-08-01

    We discuss a possibility to explain the excess of h → μτ at one-loop level. We introduce three generations of vector-like lepton doublet L‧ and two singlet scalars S1,2 which are odd under Z2, while all the standard model fields are even under this discrete symmetry. We show that S1 can be a good dark matter candidate. We show that we can explain the dark matter relic abundance, large part of the discrepancy of muon g - 2 between experiments and the standard model predictions, as well as the h → μτ excess of ∼ 1%, while evading constraints from experiments of dark matter direct detection and charged lepton flavor violating processes. We also consider prospects of production of S2 at LHC with energy √{ s} = 14 TeV.

  10. Collision-Induced Dissociation Fragmentation Inside Disulfide C-Terminal Loops of Natural Non-Tryptic Peptides

    NASA Astrophysics Data System (ADS)

    Samgina, Tatiana Y.; Vorontsov, Egor A.; Gorshkov, Vladimir A.; Artemenko, Konstantin A.; Zubarev, Roman A.; Ytterberg, Jimmy A.; Lebedev, Albert T.

    2013-07-01

    Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.

  11. Structure of the Neisserial outer membrane protein Opa₆₀: loop flexibility essential to receptor recognition and bacterial engulfment.

    PubMed

    Fox, Daniel A; Larsson, Per; Lo, Ryan H; Kroncke, Brett M; Kasson, Peter M; Columbus, Linda

    2014-07-16

    The structure and dynamics of Opa proteins, which we report herein, are responsible for the receptor-mediated engulfment of Neisseria gonorrheae or Neisseria meningitidis by human cells and can offer deep understanding into the molecular recognition of pathogen-host receptor interactions. Such interactions are vital to understanding bacterial pathogenesis as well as the mechanism of foreign body entry to a human cell, which may provide insights for the development of targeted pharmaceutical delivery systems. The size and dynamics of the extracellular loops of Opa60 required a hybrid refinement approach wherein membrane and distance restraints were used to generate an initial NMR structural ensemble, which was then further refined using molecular dynamics in a DMPC bilayer. The resulting ensemble revealed that the extracellular loops, which bind host receptors, occupy compact conformations, interact with each other weakly, and are dynamic on the nanosecond time scale. We predict that this conformational sampling is critical for enabling diverse Opa loop sequences to engage a common set of receptors.

  12. Structure of the Neisserial outer membrane protein Opa₆₀: loop flexibility essential to receptor recognition and bacterial engulfment.

    PubMed

    Fox, Daniel A; Larsson, Per; Lo, Ryan H; Kroncke, Brett M; Kasson, Peter M; Columbus, Linda

    2014-07-16

    The structure and dynamics of Opa proteins, which we report herein, are responsible for the receptor-mediated engulfment of Neisseria gonorrheae or Neisseria meningitidis by human cells and can offer deep understanding into the molecular recognition of pathogen-host receptor interactions. Such interactions are vital to understanding bacterial pathogenesis as well as the mechanism of foreign body entry to a human cell, which may provide insights for the development of targeted pharmaceutical delivery systems. The size and dynamics of the extracellular loops of Opa60 required a hybrid refinement approach wherein membrane and distance restraints were used to generate an initial NMR structural ensemble, which was then further refined using molecular dynamics in a DMPC bilayer. The resulting ensemble revealed that the extracellular loops, which bind host receptors, occupy compact conformations, interact with each other weakly, and are dynamic on the nanosecond time scale. We predict that this conformational sampling is critical for enabling diverse Opa loop sequences to engage a common set of receptors. PMID:24813921

  13. Detailed computational analysis revealed mutation V210I on PrP induced conformational conversion on β2-α2 loop and α2-α3.

    PubMed

    Chandrasekaran, P; Rajasekaran, R

    2016-10-20

    The development of fatal transmissible spongiform encephalopathies (TSE) is associated with the conformational conversion of the normal cellular prion protein, PrP(C), into its pathogenic isoform, PrP(Sc). The present study revealed the structural consequences that induce the conversion of PrP(C)→ PrP(Sc) upon mutation V210I linked with genetic Creutzfeldt-Jakob disease (CJD) using the classical molecular dynamics (MD) approach. Similar to the experimental results, the mutant showed biased disruption in the local folding of α2 and the complete distortion of α3. In addition, substitution of bulkier Ile at position 210 induced reorientations of several residues that were the constituent of hydrophobic cores, thereby influencing α2-α3 inter-helical interactions. In addition, the β2-α2 loop was greatly altered due to the loss of π-π interactions of the residue Tyr(169) with Phe(175), Tye(163), Tyr(162), and Tyr(218), facilitating more conformational flexibility, which may be involved in the conversion of PrP(C)→ PrP(Sc). This study afforded a detailed structure and dynamic properties of the mutant, which were consistent with the experimental results, providing an insight into the molecular basis for the conversion of PrP(C)→ PrP(Sc), which could be used for the development of antiprion drugs. PMID:27523988

  14. The Kinetics of Dislocation Loop Formation in Ferritic Alloys Through the Aggregation of Irradiation Induced Defects

    NASA Astrophysics Data System (ADS)

    Kohnert, Aaron Anthony

    The mechanical properties of materials are often degraded over time by exposure to irradiation environments, a phenomenon that has hindered the development of multiple nuclear reactor design concepts. Such property changes are the result of microstructural changes induced by the collision of high energy particles with the atoms in a material. The lattice defects generated in these recoil events migrate and interact to form extended damage structures. This study has used theoretical models based on the mean field chemical reaction rate theory to analyze the aggregation of isolated lattice defects into larger microstructural features that are responsible for long term property changes, focusing on the development of black dot damage in ferritic iron based alloys. The purpose of such endeavors is two-fold. Primarily, such models explain and quantify the processes through which these microstructures form. Additionally, models provide insight into the behavior and properties of the point defects and defect clusters which drive general microstructural evolution processes. The modeling effort presented in this work has focused on physical fidelity, drawing from a variety of sources of information to characterize the unobservable defect generation and agglomeration processes that give rise to the observable features reported in experimental data. As such, the models are based not solely on isolated point defect creation, as is the case with many older rate theory approaches, but instead on realistic estimates of the defect cluster population produced in high energy cascade damage events. Experimental assessments of the microstructural changes evident in transmission electron microscopy studies provide a means to measure the efficacy of the kinetic models. Using common assumptions of the mobility of defect clusters generated in cascade damage conditions, an unphysically high density of damage features develops at the temperatures of interest with a temperature dependence

  15. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.

    PubMed

    Hoang, Charmaine; Chen, Junjun; Vizthum, Caroline A; Kandel, Jason M; Hamilton, Christopher S; Mueller, Eugene G; Ferré-D'Amaré, Adrian R

    2006-11-17

    RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping.

  16. Frequency difference stabilization in dual-frequency laser by stress-induced birefringence closed-loop control.

    PubMed

    Li, Jiyang; Niu, Yanxiong; Niu, Haisha

    2016-06-01

    The frequency difference of dual-frequency lasers is increasingly becoming an area of focus in research. The stabilization of beat frequency is of significance in fields such as synthetic wavelength and shows great potential in precise measurement. In this paper, a novel device based on stress-induced birefringence closed-loop control is proposed. Experiments are carried out on a dual-frequency He-Ne Zeeman-birefringence laser with the output mirror sealed in the opposite direction. The results show that the device is capable of controlling the frequency difference variation in 1.3%, in a convenient and highly cost-effective way, and it can increase the quantity of frequency difference, which is crucial to the application of precise measurement through dual-frequency lasers.

  17. Dark-matter production through loop-induced processes at the LHC: the s-channel mediator case

    NASA Astrophysics Data System (ADS)

    Mattelaer, Olivier; Vryonidou, Eleni

    2015-09-01

    We show how studies relevant for mono-X searches at the LHC in simplified models featuring a dark-matter candidate and an s-channel mediator can be performed within the MadGraph5_aMC@NLO framework. We focus on gluon-initiated loop-induced processes, mostly relevant to the case where the mediator couples preferentially to third generation quarks and in particular to the top quark. Our implementation allows us to study signatures at hadron colliders involving missing transverse energy plus jets or plus neutral bosons (γ ,Z,H), possibly including the effects of extra radiation by multi-parton merging and matching to the parton shower.

  18. A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice

    PubMed Central

    Rössger, Katrin; Charpin-El-Hamri, Ghislaine; Fussenegger, Martin

    2013-01-01

    Diet-induced obesity is a lifestyle-associated medical condition that increases the risk of developing cardiovascular disease, type 2 diabetes and certain types of cancer. Here we report the design of a closed-loop genetic circuit that constantly monitors blood fatty acid levels in the setting of diet-associated hyperlipidemia and coordinates reversible and adjustable expression of the clinically licensed appetite-suppressing peptide hormone pramlintide. Grafting of the peroxisome proliferator-activated receptor-α onto the phloretin-responsive repressor TtgR produces a synthetic intracellular lipid-sensing receptor (LSR) that reversibly induces chimeric TtgR-specific promoters in a fatty acid-adjustable manner. Mice with diet-induced obesity in which microencapsulated cells engineered for LSR-driven expression of pramlintide are implanted show significant reduction in food consumption, blood lipid levels and body weight when put on a high-fat diet. Therapeutic designer circuits that monitor levels of pathologic metabolites and link these with the tailored expression of protein pharmaceuticals may provide new opportunities for the treatment of metabolic disorders. PMID:24281397

  19. Aircraft propeller induced structure-borne noise

    NASA Technical Reports Server (NTRS)

    Unruh, James F.

    1989-01-01

    A laboratory-based test apparatus employing components typical of aircraft construction was developed that would allow the study of structure-borne noise transmission due to propeller induced wake/vortex excitation of in-wake structural appendages. The test apparatus was employed to evaluate several aircraft installation effects (power plant placement, engine/nacelle mass loading, and wing/fuselage attachment methods) and several structural response modifications for structure-borne noise control (the use of wing blocking mass/fuel, wing damping treaments, and tuned mechanical dampers). Most important was the development of in-flight structure-borne noise transmission detection techniques using a combination of ground-based frequency response function testing and in-flight structural response measurement. Propeller wake/vortex excitation simulation techniques for improved ground-based testing were also developed to support the in-flight structure-borne noise transmission detection development.

  20. Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

    PubMed

    Rysavy, Steven J; Beck, David A C; Daggett, Valerie

    2014-11-01

    Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments.

  1. The structure of fast sausage waves in current-carrying coronal loops

    NASA Astrophysics Data System (ADS)

    Bembitov, D. B.; Mikhalyaev, B. B.; Ruderman, M. S.

    2014-09-01

    We study fast sausage waves in a model coronal loop that consists of a cylindrical core with axial magnetic field and coaxial annulus with purely azimuthal magnetic field. The magnetic field is discontinuous at the tube and core boundaries, and there are surface currents with the opposite directions on these boundaries. The principal mode of fast sausage waves in which the magnetic pressure perturbation has no nodes in the radial direction can exist for arbitrary wavelength. The results for the fundamental radial mode of sausage waves are applied to the interpretation of observed periodic pulsations of microwave emission in flaring loops with periods of a few tens of seconds. Radial plasma motion has opposite directions at the tube and core boundaries. This leads to the periodic contraction and expansion of the annulus. We assume that the principal mode of fast sausage waves in the current-carrying coronal loops is able to produce a current sheet. However, the nonlinear analysis is needed to confirm this conjecture.

  2. Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y-27632.

    PubMed

    Yamaguchi, Hiroto; Miwa, Yukiko; Kasa, Miyuki; Kitano, Ken; Amano, Mutsuki; Kaibuchi, Kozo; Hakoshima, Toshio

    2006-09-01

    Rho-kinase is a main player in the regulation of cytoskeletal events and a promising drug target in the treatment of both vascular and neurological disorders. Here we report the crystal structure of the Rho-kinase catalytic domain in complex with the specific inhibitor Y-27632. Comparison with the structure of PKA bound to this inhibitor revealed a potential induced-fit binding mode that can be accommodated by the phosphate binding loop. This binding mode resembles to that observed in the Rho-kinase-fasudil complex. A structural database search indicated that a pocket underneath the phosphate-binding loop is present that favors binding to a small aromatic ring. Introduction of such a ring group might spawn a new modification scheme of pre-existing protein kinase inhibitors for improved binding capability. PMID:16891330

  3. An investigation of coronal active region loop structures using AS&E rocket X-ray images

    NASA Technical Reports Server (NTRS)

    Webb, D. F.

    1983-01-01

    Simultaneous high spatial resolution observations at 6 cm in soft X-rays, in photospheric magnetograms, and in optical filtergrams were used to compare the most intense sources of centimetric emission in two active regions to coronal loops, sunspots, chromospheric structures, and photospheric magnetic fields. Results show that the majority of the bright microwave components are not associated with sunspots or X-ray emission. A nonthermal mechanism appears necessary to explain the brightest microwave components, discrete regions of continuous particle acceleration may be common in active regions. Studies of the plasma parameters of selected loops imply that the radio emission is consistent with gyro-resonance absorption at the third and fourth harmonic, at least from part of each loop. Results are presented for: (1) X-ray and microwave observations of active regions; (2) comparison of coronal holes observed in soft X-rays and Hel 10830 A spectrosheliograms; and (3) the reappearance of polar coronal holes and the evolution of the solar magnetic field.

  4. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase

    PubMed Central

    Paës, Gabriel; Cortés, Juan; Siméon, Thierry; O'Donohue, Michael J.; Tran, Vinh

    2012-01-01

    Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis. PMID:24688637

  5. Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

    PubMed Central

    2015-01-01

    The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5′-rUGACU loop of the isolated SLV has been shown to adopt a Mg2+-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg2+ ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg2+-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg2+-bound loop structure. We propose this structure is a “gatekeeper” or precursor to Mg2+ binding when those ions are present. PMID:26328924

  6. Quantum tensor product structures are observable induced.

    PubMed

    Zanardi, Paolo; Lidar, Daniel A; Lloyd, Seth

    2004-02-13

    It is argued that the partition of a quantum system into subsystems is dictated by the set of operationally accessible interactions and measurements. The emergence of a multipartite tensor product structure of the state space and the associated notion of quantum entanglement are then relative and observable induced. We develop a general algebraic framework aimed to formalize this concept.

  7. Lipopolysaccharide induces the expression of an autocrine prolactin loop enhancing inflammatory response in monocytes

    PubMed Central

    2013-01-01

    Background Prolactin from pituitary gland helps maintain homeostasis but it is also released in immune cells where its function is not completely understood. Pleiotropic functions of prolactin (PRL) might be mediated by different isoforms of its receptor (PRLr). Methods The aim of this study was to investigate the relationship between the eventual synthesis of PRL and PRLr isoforms with the inflammatory response in monocytes. We used THP-1 and monocytes isolated from healthy subjects stimulated with lipopolysaccharide (LPS). Western blot, real time PCR and immunocytochemistry were performed to identify both molecules. The bioactivity of the PRL was assessed using a bioassay and ELISA to detect pro inflammatory cytokines. Results PRLr mRNA and PRL mRNA were synthesized in THP-1 monocytes activated with LPS with peaks of 300-fold and 130-fold, respectively. The long (100 kDa) and the intermediate (50 kDa) isoforms of PRLr and big PRL (60 kDa) were time-dependent upregulated for monocytes stimulated with LPS. This expression was confirmed in monocytes from healthy subjects. The PRLr intermediate isoform and the big PRL were found soluble in the culture media and later in the nucleus in THP-1 monocytes stimulated with LPS. Big PRL released by monocytes showed bioactivity in Nb2 Cells, and both PRL and PRLr, synthesized by monocytes were related with levels of nitrites and proinflammatory citokines. Conclusions Our results suggest the expression of a full-autocrine loop of PRL enhances the inflammatory response in activated monocytes. This response mediated by big PRL may contribute to the eradication of potential pathogens during innate immune response in monocytes but may also contribute to inflammatory disorders. PMID:23731754

  8. Structural analysis of the active sites of dihydrofolate reductase from two species of Candida uncovers ligand-induced conformational changes shared among species

    PubMed Central

    Paulsen, Janet L.; Viswanathan, Kishore; Wright, Dennis L.; Anderson, Amy C.

    2013-01-01

    A novel strategy for targeting the pathogenic organisms Candida albicans and Candida glabrata focuses on the development of potent and selective antifolates effective against dihydrofolate reductase. Crystal structure analysis suggested that an essential loop at the active site (Thr 58-Phe 66) differs from the analogous residues in the human enzyme, potentially providing a mechanism for achieving selectivity. In order to probe the role of this loop, we employed chemical synthesis, crystal structure determination and molecular dynamics simulations. The results of these analyses show that the loop residues undergo ligand-induced conformational changes that are similar among the fungal and human species. PMID:23375226

  9. Quantum Structure of Field Theory and Standard Model Based on Infinity-Free Loop Regularization/renormalization

    NASA Astrophysics Data System (ADS)

    Wu, Yue-Liang

    2014-02-01

    To understand better the quantum structure of field theory and standard model in particle physics, it is necessary to investigate carefully the divergence structure in quantum field theories (QFTs) and work out a consistent framework to avoid infinities. The divergence has got us into trouble since developing quantum electrodynamics in 1930s. Its treatment via the renormalization scheme is satisfied not by all physicists, like Dirac and Feynman who have made serious criticisms. The renormalization group analysis reveals that QFTs can in general be defined fundamentally with the meaningful energy scale that has some physical significance, which motivates us to develop a new symmetry-preserving and infinity-free regularization scheme called loop regularization (LORE). A simple regularization prescription in LORE is realized based on a manifest postulation that a loop divergence with a power counting dimension larger than or equal to the space-time dimension must vanish. The LORE method is achieved without modifying original theory and leads the divergent Feynman loop integrals well-defined to maintain the divergence structure and meanwhile preserve basic symmetries of original theory. The crucial point in LORE is the presence of two intrinsic energy scales which play the roles of ultraviolet cutoff Mc and infrared cutoff μs to avoid infinities. As Mc can be made finite when taking appropriately both the primary regulator mass and number to be infinity to recover the original integrals, the two energy scales Mc and μs in LORE become physically meaningful as the characteristic energy scale and sliding energy scale, respectively. The key concept in LORE is the introduction of irreducible loop integrals (ILIs) on which the regularization prescription acts, which leads to a set of gauge invariance consistency conditions between the regularized tensor-type and scalar-type ILIs. An interesting observation in LORE is that the evaluation of ILIs with ultraviolet

  10. Quantum Structure of Field Theory and Standard Model Based on Infinity-Free Loop Regularization/renormalization

    NASA Astrophysics Data System (ADS)

    Wu, Yue-Liang

    2014-04-01

    To understand better the quantum structure of field theory and standard model in particle physics, it is necessary to investigate carefully the divergence structure in quantum field theories (QFTs) and work out a consistent framework to avoid infinities. The divergence has got us into trouble since developing quantum electrodynamics in 1930s. Its treatment via the renormalization scheme is satisfied not by all physicists, like Dirac and Feynman who have made serious criticisms. The renormalization group analysis reveals that QFTs can in general be defined fundamentally with the meaningful energy scale that has some physical significance, which motivates us to develop a new symmetry-preserving and infinity-free regularization scheme called loop regularization (LORE). A simple regularization prescription in LORE is realized based on a manifest postulation that a loop divergence with a power counting dimension larger than or equal to the space-time dimension must vanish. The LORE method is achieved without modifying original theory and leads the divergent Feynman loop integrals well-defined to maintain the divergence structure and meanwhile preserve basic symmetries of original theory. The crucial point in LORE is the presence of two intrinsic energy scales which play the roles of ultraviolet cutoff Mc and infrared cutoff μs to avoid infinities. As Mc can be made finite when taking appropriately both the primary regulator mass and number to be infinity to recover the original integrals, the two energy scales Mc and μs in LORE become physically meaningful as the characteristic energy scale and sliding energy scale, respectively. The key concept in LORE is the introduction of irreducible loop integrals (ILIs) on which the regularization prescription acts, which leads to a set of gauge invariance consistency conditions between the regularized tensor-type and scalar-type ILIs. An interesting observation in LORE is that the evaluation of ILIs with ultraviolet

  11. Mutant OmpF porins of Yersinia pseudotuberculosis with deletions of external loops: structure-functional and immunochemical properties.

    PubMed

    Sidorova, O V; Khomenko, V A; Portnyagina, O Yu; Likhatskaya, G N; Vakorina, T I; Kim, N Yu; Chistyulin, D K; Solov'eva, T F; Novikova, O D

    2014-03-01

    Recombinant mutant OmpF porins from Yersinia pseudotuberculosis outer membrane were obtained using site-directed mutagenesis. Here we used four OmpF mutants where single extracellular loops L1, L4, L6, and L8 were deleted one at a time. The proteins were expressed in Escherichia coli at levels comparable to full-sized recombinant OmpF porin and isolated from the inclusion bodies. Purified trimers of the mutant porins were obtained after dialysis and consequent ion-exchange chromatography. Changes in molecular and spatial structure of the mutants obtained were studied using SDS-PAGE and optical spectroscopy (circular dichroism and intrinsic protein fluorescence). Secondary and tertiary structure of the mutant proteins was found to have some features in comparison with that of the full-sized recombinant OmpF. As shown by bilayer lipid membrane technique, the pore-forming activity of purified mutant porins was identical to OmpF porin isolated from the bacterial outer membrane. Lacking of the external loops mentioned above influenced significantly upon the antigenic structure of the porin as demonstrated using ELISA.

  12. Higgs-Strahlung: Merging the NLO Drell-Yan and loop-induced 0 +1 jet multiplicities

    NASA Astrophysics Data System (ADS)

    Gonçalves, Dorival; Krauss, Frank; Kuttimalai, Silvan; Maierhöfer, Philipp

    2015-10-01

    We analyze the production of a Higgs boson in association with a Z boson at hadron colliders in the Standard Model and some simple extensions. We show how multijet merging algorithms at leading and next-to-leading order for the loop-induced gluon fusion and the Drell-Yan-like quark-induced processes, respectively, improve the descriptions for various differential distributions, in particular those that involve the production of additional jets. The phenomenological studies focus on two relevant channels of Higgs boson decays, namely H →invisible and H →b b ¯. We find sizable and phenomenologically relevant corrections to the transverse momentum and invariant mass distributions for the Higgs boson candidate. Thanks to the large destructive interference for the top Yukawa terms, this process is very sensitive to the magnitude and sign of a possible nonstandard top-Higgs coupling. We analyze the impact of this anomalous interaction on distributions and estimate constraints from LHC Run II.

  13. Thermally induced all-optical inverter and dynamic hysteresis loops in graphene oxide dispersions.

    PubMed

    Melle, Sonia; Calderón, Oscar G; Egatz-Gómez, Ana; Cabrera-Granado, E; Carreño, F; Antón, M A

    2015-11-01

    We experimentally study the temporal dynamics of amplitude-modulated laser beams propagating through a water dispersion of graphene oxide sheets in a fiber-to-fiber U-bench. Nonlinear refraction induced in the sample by thermal effects leads to both phase reversing of the transmitted signals and dynamic hysteresis in the input-output power curves. A theoretical model including beam propagation and thermal lensing dynamics reproduces the experimental findings. PMID:26560566

  14. DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean.

    PubMed

    Xodo, L E; Manzini, G; Quadrifoglio, F; van der Marel, G; van Boom, J

    1991-04-11

    Hairpin structures formed by seven DNA inverted repeats have been studied by PAGE, UV(CD)-spectroscopy and nuclease cleavage. The hairpins consisted of (CG)3 stems and loops of 2, 3 and 4 residues. Thermal stabilities (Tm) have been determined in low and high ionic strength buffers, where the hairpins were structured in the B- and Z-DNA form respectively. The thermodynamic parameters of hairpin formation have been obtained by a two-state analysis of the hairpin-coil transitions. It is found that, on increasing the number of bases in the loop from 2 to 3 and 4, the Tms of the B-hairpins decrease, whereas the Tms of the same hairpins in the Z-form increase. This confirms previous evidence (1,2) that in a hairpin molecule the size and structure of the loop are modulated by the conformation of the helical stem. Moreover, B-hairpins with loops comprising 2, 3 and 4 bases have been digested with the single-strand-specific nuclease from mung bean. In our experimental conditions (0 degrees C) the nuclease preferentially cleaves the unbonded nucleotides of the loops. However, the rates of loop hydrolysis, which roughly follow a first-order kinetics, markedly depend on the size of the loop. At a ratio of 3 enzyme units/micrograms DNA, the half-lives of hairpins which are expected to form loops of 4, 3 and 2 residues are 90, 145 and 440 minutes respectively. Thermostability and enzymatic digestion data suggest that two-membered loops can be formed in B-hairpins but not in Z-hairpins. PMID:2027758

  15. Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns.

    PubMed

    Znosko, Brent M; Kennedy, Scott D; Wille, Pamela C; Krugh, Thomas R; Turner, Douglas H

    2004-12-21

    The J4/5 loop of group I introns has tertiary interactions with the P1 helix that position the P1 substrate for the self-splicing reaction. The J4/5 loop of Candida albicans and Candida dubliniensis, 5'GAAGG3'/3'UAAUU5', potentially contains two A.A pairs flanked by one G.U pair on one side and two G.U pairs on the other side. Results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments with a mimic of the C. albicans and C. dubliniensis J4/5 loop are consistent with the adenosines forming tandem sheared A.A pairs with a cross-strand stack and only the G.U pair not adjacent to an A.A pair forming a static wobble G.U pair. The two G.U pairs adjacent to the tandem A.A pairs are likely in a dynamic equilibrium between multiple conformations. Although Co(NH(3))(6)(3+) stabilizes the loop by several kilocalories per mole at 37 degrees C, addition of Mg(2+) or Co(NH(3))(6)(3+) has no effect on the structure of the loop. The tandem G.U pairs provide a pocket of negative charge for Co(NH(3))(6)(3+) to bind. The results contribute to understanding the structure and dynamics of purine-rich internal loops and potential G.U pairs adjacent to internal loops.

  16. Structural characterization of d(CAACCCGTTG) and d(CAACGGGTTG) mini-hairpin loops by heteronuclear NMR: the effects of purines versus pyrimidines in DNA hairpins.

    PubMed Central

    Avizonis, D Z; Kearns, D R

    1995-01-01

    The DNA decamers, d(CAACCCGTTG) and d(CAACGGGTTG) were studied in solution by proton and heteronuclear NMR. Under appropriate conditions of pH, temperature, salt concentration and DNA concentration, both decamers form hairpin conformations with similar stabilities [Avizonis and Kearns (1995) Biopolymers, 35, 187-200]. Both decamers adopt mini-hairpin loops, where the first and last four nucleotides are involved in Watson-Crick hydrogen bonding and the central two nucleotides, CC or GG respectively, form the loop. Through the use of proton-proton, proton-phosphorus and natural abundance proton-carbon NMR experiments, backbone torsion angles (beta, gamma and epsilon), sugar puckers and interproton distances were measured. The nucleotides forming the loops of these decamers were found to stack upon one another in an L1 type of loop conformation. Both show gamma tr and unusual beta torsion angles in the loop-closing nucleotide G7, as expected for mini-hairpin loop formation. Our results indicate that the beta and epsilon torsion angles of the fifth and sixth nucleotides that form the loop and the loop-closing nucleotide G7 are not in the standard trans conformation as found in B-DNA. Although the loop structures calculated from NMR-derived constraints are not well defined, the stacking of the bases in the two different hairpins is different. This difference in the base stacking of the loop may provide an explanation as to why the cytosine-containing hairpin is thermodynamically more stable than the guanine-containing hairpin. PMID:7739905

  17. Robust Feedback Control of Flow Induced Structural Radiation of Sound

    NASA Technical Reports Server (NTRS)

    Heatwole, Craig M.; Bernhard, Robert J.; Franchek, Matthew A.

    1997-01-01

    A significant component of the interior noise of aircraft and automobiles is a result of turbulent boundary layer excitation of the vehicular structure. In this work, active robust feedback control of the noise due to this non-predictable excitation is investigated. Both an analytical model and experimental investigations are used to determine the characteristics of the flow induced structural sound radiation problem. The problem is shown to be broadband in nature with large system uncertainties associated with the various operating conditions. Furthermore the delay associated with sound propagation is shown to restrict the use of microphone feedback. The state of the art control methodologies, IL synthesis and adaptive feedback control, are evaluated and shown to have limited success for solving this problem. A robust frequency domain controller design methodology is developed for the problem of sound radiated from turbulent flow driven plates. The control design methodology uses frequency domain sequential loop shaping techniques. System uncertainty, sound pressure level reduction performance, and actuator constraints are included in the design process. Using this design method, phase lag was added using non-minimum phase zeros such that the beneficial plant dynamics could be used. This general control approach has application to lightly damped vibration and sound radiation problems where there are high bandwidth control objectives requiring a low controller DC gain and controller order.

  18. Usefulness of implantable loop recorders in office-based practice for evaluation of syncope in patients with and without structural heart disease.

    PubMed

    Mason, Pamela K; Wood, Mark A; Reese, Daniel B; Lobban, John H; Mitchell, Mark A; DiMarco, John P

    2003-11-01

    Early use of an implantable loop recorder for evaluating unexplained syncope in an office-based electrophysiology practice is an effective approach in patients with and without structural heart disease. Documentation of rhythm with an implantable loop recorder at the time of symptoms is possible in approximately 50% and 80% of patients in both groups after 1 and 2 years of follow-up, respectively. PMID:14583373

  19. THE SPECIFIC ACCELERATION RATE IN LOOP-STRUCTURED SOLAR FLARES-IMPLICATIONS FOR ELECTRON ACCELERATION MODELS

    SciTech Connect

    Guo, Jingnan; Emslie, A. Gordon; Piana, Michele E-mail: piana@dima.unige.it

    2013-03-20

    We analyze electron flux maps based on RHESSI hard X-ray imaging spectroscopy data for a number of extended coronal-loop flare events. For each event, we determine the variation of the characteristic loop length L with electron energy E, and we fit this observed behavior with models that incorporate an extended acceleration region and an exterior 'propagation' region, and which may include collisional modification of the accelerated electron spectrum inside the acceleration region. The models are characterized by two parameters: the plasma density n in, and the longitudinal extent L{sub 0} of, the acceleration region. Determination of the best-fit values of these parameters permits inference of the volume that encompasses the acceleration region and of the total number of particles within it. It is then straightforward to compute values for the emission filling factor and for the specific acceleration rate (electrons s{sup -1} per ambient electron above a chosen reference energy). For the 24 events studied, the range of inferred filling factors is consistent with a value of unity. The inferred mean value of the specific acceleration rate above E{sub 0} = 20 keV is {approx}10{sup -2} s{sup -1}, with a 1{sigma} spread of about a half-order-of-magnitude above and below this value. We compare these values with the predictions of several models, including acceleration by large-scale, weak (sub-Dreicer) fields, by strong (super-Dreicer) electric fields in a reconnecting current sheet, and by stochastic acceleration processes.

  20. Structural switching of Cu,Zn-superoxide dismutases at loop VI: insights from the crystal structure of 2-mercaptoethanol-modified enzyme

    PubMed Central

    Ihara, Kentaro; Fujiwara, Noriko; Yamaguchi, Yoshiki; Torigoe, Hidetaka; Wakatsuki, Soichi; Taniguchi, Naoyuki; Suzuki, Keiichiro

    2012-01-01

    Cu,Zn SOD1 (superoxide dismutase 1) is implicated in FALS (familial amyotrophic lateral sclerosis) through the accumulation of misfolded proteins that are toxic to neuronal cells. Loop VI (residues 102–115) of the protein is at the dimer interface and could play a critical role in stability. The free cysteine residue, Cys111 in the loop, is readily oxidized and alkylated. We have found that modification of this Cys111 with 2-ME (2-mercaptoethanol; 2-ME-SOD1) stabilizes the protein and the mechanism may provide insights into destabilization and the formation of aggregated proteins. Here, we determined the crystal structure of 2-ME-SOD1 and find that the 2-ME moieties in both subunits interact asymmetrically at the dimer interface and that there is an asymmetric configuration of segment Gly108 to Cys111 in loop VI. One loop VI of the dimer forms a 310-helix (Gly108 to His110) within a unique β-bridge stabilized by a hydrogen bond between Ser105-NH and His110-CO, while the other forms a β-turn without the H-bond. The H-bond (H-type) and H-bond free (F-type) configurations are also seen in some wild-type and mutant human SOD1s in the Protein Data Bank suggesting that they are interconvertible and an intrinsic property of SOD1s. The two structures serve as a basis for classification of these proteins and hopefully a guide to their stability and role in pathophysiology. PMID:22804629

  1. Reduction of enterotoxin induced fluid accumulation in ileal loops of neonatal calves with anti-F5 fimbriae recombinant antibody.

    PubMed

    Sahagun-Ruiz, Alfredo; Velazquez, Leticia V; Bhaskaran, Shoba; Jay, Chris M; Morales-Salinas, E; Rathore, Keerti; Wagner, Gale G; Waghela, Suryakant D

    2015-12-01

    Neonatal calf colibacillosis caused by enterotoxigenic Escherichia coli (ETEC) is an economically significant problem in most parts of the world. The most common ETEC found in calves express the F5 (K99) fimbriae, which are necessary for the attachment of the bacteria to the ganglioside receptors on enterocytes. It is known that prevention of ETEC F5(+) adhesion to its ganglioside receptors with specific antibodies protects calves from colibacillosis. Previously we have described the development and characterization of a mouse recombinant antibody fragment (moRAb) that prevents F5 fimbrial protein induced agglutination of horse red blood cells (HRBC), which exhibit the same gangloside receptor for F5 fimbriae. Here we demonstrate that this recombinant antibody fragment inhibits in vitro the attachment of ETEC F5(+) bacteria to HRBC as well as isolated calf enterocytes, and in vivo it decreases fluid accumulation in intestinal loops of calves. Thus, correct oral administration of this anti-F5 moRAb may serve as an immunoprophylactic for cost effective control of colibacillosis in calves. PMID:26521056

  2. Artemisinin induces A549 cell apoptosis dominantly via a reactive oxygen species-mediated amplification activation loop among caspase-9, -8 and -3.

    PubMed

    Gao, Weijie; Xiao, Fenglian; Wang, Xiaoping; Chen, Tongsheng

    2013-10-01

    This report is designed to explore the roles of caspase-8, -9 and -3 in artemisinin (ARTE)-induced apoptosis in non-small cell lung cancer cells (A549 cells). ARTE induced reactive oxygen species (ROS)-mediated apoptosis in dose- and time-dependent fashion. Although ARTE treatment did not induce Bid cleavage and significant loss of mitochondrial membrane potential, it induced release of Smac and AIF but not cytochrome c from mitochondria, and silencing of Bak but not Bax significantly prevented ARTE-induced cytotoxicity. Moreover, ARTE treatment induced ROS-dependent activation of caspase-9, -8 and -3. Of the utmost importance, silencing or inhibiting any one of caspase-8, -9 and -3 almost completely prevented ARTE-induced activation of all the three caspases and remarkably abrogated the cytotoxicity of ARTE, suggesting that ARTE triggered an amplification activation loop among caspase-9, -8 and -3. Collectively, our data demonstrate that ARTE induces a ROS-mediated amplification activation loop among caspase-9, -8 and -3 to dominantly mediate the apoptosis of A549 cells. PMID:23661289

  3. Artemisinin induces A549 cell apoptosis dominantly via a reactive oxygen species-mediated amplification activation loop among caspase-9, -8 and -3.

    PubMed

    Gao, Weijie; Xiao, Fenglian; Wang, Xiaoping; Chen, Tongsheng

    2013-10-01

    This report is designed to explore the roles of caspase-8, -9 and -3 in artemisinin (ARTE)-induced apoptosis in non-small cell lung cancer cells (A549 cells). ARTE induced reactive oxygen species (ROS)-mediated apoptosis in dose- and time-dependent fashion. Although ARTE treatment did not induce Bid cleavage and significant loss of mitochondrial membrane potential, it induced release of Smac and AIF but not cytochrome c from mitochondria, and silencing of Bak but not Bax significantly prevented ARTE-induced cytotoxicity. Moreover, ARTE treatment induced ROS-dependent activation of caspase-9, -8 and -3. Of the utmost importance, silencing or inhibiting any one of caspase-8, -9 and -3 almost completely prevented ARTE-induced activation of all the three caspases and remarkably abrogated the cytotoxicity of ARTE, suggesting that ARTE triggered an amplification activation loop among caspase-9, -8 and -3. Collectively, our data demonstrate that ARTE induces a ROS-mediated amplification activation loop among caspase-9, -8 and -3 to dominantly mediate the apoptosis of A549 cells.

  4. NOTCH3 expression is induced in mural cells through an autoregulatory loop that requires endothelial-expressed JAGGED1.

    PubMed

    Liu, Hua; Kennard, Simone; Lilly, Brenda

    2009-02-27

    Endothelial cells and mural cells (smooth muscle cells, pericytes, or fibroblasts) are known to communicate with one another. Their interactions not only serve to support fully functional blood vessels but also can regulate vessel assembly and differentiation or maturation. In an effort to better understand the molecular components of this heterotypic interaction, we used a 3D model of angiogenesis and screened for genes, which were modulated by coculturing of these 2 different cell types. In doing so, we discovered that NOTCH3 is one gene whose expression is robustly induced in mural cells by coculturing with endothelial cells. Knockdown by small interfering RNA revealed that NOTCH3 is necessary for endothelial-dependent mural cell differentiation, whereas overexpression of NOTCH3 is sufficient to promote smooth muscle gene expression. Moreover, NOTCH3 contributes to the proangiogenic abilities of mural cells cocultured with endothelial cells. Interestingly, we found that the expression of NOTCH3 is dependent on Notch signaling, because the gamma-secretase inhibitor DAPT blocked its upregulation. Furthermore, in mural cells, a dominant-negative Mastermind-like1 construct inhibited NOTCH3 expression, and endothelial-expressed JAGGED1 was required for its induction. Additionally, we demonstrated that NOTCH3 could promote its own expression and that of JAGGED1 in mural cells. Taken together, these data provide a mechanism by which endothelial cells induce the differentiation of mural cells through activation and induction of NOTCH3. These findings also suggest that NOTCH3 has the capacity to maintain a differentiated phenotype through a positive-feedback loop that includes both autoregulation and JAGGED1 expression.

  5. Telomere targeting with a novel G-quadruplex-interactive ligand BRACO-19 induces T-loop disassembly and telomerase displacement in human glioblastoma cells.

    PubMed

    Zhou, Guangtong; Liu, Xinrui; Li, Yunqian; Xu, Songbai; Ma, Chengyuan; Wu, Xinmin; Cheng, Ye; Yu, Zhiyun; Zhao, Gang; Chen, Yong

    2016-03-22

    Interference with telomerase and telomere maintenance is emerging as an attractive target for anticancer therapies. Ligand-induced stabilization of G-quadruplex formation by the telomeric DNA 3'-overhang inhibits telomerase from catalyzing telomeric DNA synthesis and from capping telomeric ends, making these ligands good candidates for chemotherapeutic purposes. BRACO-19 is one of the most effective and specific ligand for telomeric G4. It is shown here that BRACO-19 suppresses proliferation and reduces telomerase activity in human glioblastoma cells, paralleled by the displacement of telomerase from nuclear to cytoplasm. Meanwhile, BRACO-19 triggers extensive DNA damage response at telomere, which may result from uncapping and disassembly of telomeric T-loop structure, characterized by the formation of anaphase bridge and telomere fusion, as well as the release of telomere-binding protein from telomere. The resulting dysfunctional telomere ultimately provokes p53 and p21-mediated cell cycle arrest, apoptosis and senescence. Notably, normal primary astrocytes do not respond to the treatment of BRACO-19, suggesting the agent's good selectivity for cancer cells. These results reinforce the notion that G-quadruplex binding compounds can act as broad inhibitors of telomere-related processes and have potential as selective antineoplastic drugs for various tumors including malignant gliomas. PMID:26908447

  6. Induced cycle structures of the hyperoctahedral group

    SciTech Connect

    Chen, W.Y.C.

    1992-06-01

    The hyperoctahedral group B{sub n} is treated as the automorphism group of the n-dimensional hypercube, denoted Q{sub n}, which is nowadays understood to be a graph on 2{sup n} vertices. It is well-known that B{sub n} can be represented by the group of signed permutations. In other words, any signed permutation induces a permutation on the vertices of Q{sub n} which preserves adjacencies. Moreover, signed permutations also a permutation group on the edge of Q{sub n}, denoted H{sub n}. We study the cycle structures of both B{sub n} and H{sub n}. The technique proposed here is to determine the induced cycle structure of a signed permutation by the number of fixed vertices or fixed edges of a signed permutation in the cyclic group generated by a signed permutation of given type. Here we directly define the type of a signed permutation by a double partition based on its signed cycle decomposition. In this way, we obtain explicit formulas for the number of induced cycles on vertices as well as edges of Q{sub n} of a signed permutation in terms of its type. By further exploring the connection between cycle indices and the structure of fixed points, we obtain the cycle indices of both B{sub n} and H{sub n}. Our formula for the cycle index of B{sub n}is much more natural and considerably simpler than that of Harrison and High. Meanwhile, the cycle structure of H{sub n} seems to have been untouched before, although it is well motivated by nonisomorphic edge colorings of Q{sub n} as well as by the recent interest in symmetries of computer networks.

  7. Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1.

    PubMed

    van den Boom, Johannes; Trusch, Franziska; Hoppstock, Lukas; Beuck, Christine; Bayer, Peter

    2016-01-01

    Type 2 asparaginases, a subfamily of N-terminal nucleophile (Ntn) hydrolases, are activated by limited proteolysis. This activation yields a heterodimer and a loop region at the C-terminus of the α-subunit is released. Since this region is unresolved in all type 2 asparaginase crystal structures but is close to the active site residues, we explored this loop region in six members of the type 2 asparaginase family using homology modeling. As the loop model for the childhood cancer-relevant protease Taspase1 differed from the other members, Taspase1 activation as well as the conformation and dynamics of the 56 amino acids loop were investigated by CD and NMR spectroscopy. We propose a helix-turn-helix motif, which can be exploited as novel anticancer target to inhibit Taspase1 proteolytic activity. PMID:26974973

  8. Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1

    PubMed Central

    van den Boom, Johannes; Trusch, Franziska; Hoppstock, Lukas; Beuck, Christine; Bayer, Peter

    2016-01-01

    Type 2 asparaginases, a subfamily of N-terminal nucleophile (Ntn) hydrolases, are activated by limited proteolysis. This activation yields a heterodimer and a loop region at the C-terminus of the α-subunit is released. Since this region is unresolved in all type 2 asparaginase crystal structures but is close to the active site residues, we explored this loop region in six members of the type 2 asparaginase family using homology modeling. As the loop model for the childhood cancer-relevant protease Taspase1 differed from the other members, Taspase1 activation as well as the conformation and dynamics of the 56 amino acids loop were investigated by CD and NMR spectroscopy. We propose a helix-turn-helix motif, which can be exploited as novel anticancer target to inhibit Taspase1 proteolytic activity. PMID:26974973

  9. Phase transition and hysteresis loop in structured games with global updating

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Xu; Lü, Jinhu; Chen, Guanrong; Hui, P. M.

    2008-04-01

    We present a global payoff-based strategy updating model for studying cooperative behavior of a networked population. We adopt the Prisoner’s Dilemma game and the snowdrift game as paradigms for characterizing the interactions among individuals. We investigate the model on regular, small-world, and scale-free networks, and find multistable cooperation states depending on the initial cooperator density. In particular for the snowdrift game on small-world and scale-free networks, there exist a discontinuous phase transition and hysteresis loops of cooperator density. We explain the observed properties by theoretical predictions and simulation results of the average number of neighbors of cooperators and defectors, respectively. Our work indicates that individuals with more neighbors have a trend to preserve their initial strategies, which has strong impacts on the strategy updating of individuals with fewer neighbors; while the fact that individuals with few neighbors have to become cooperators to avoid gaining the lowest payoff plays significant roles in maintaining and spreading of cooperation strategy.

  10. Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

    PubMed Central

    Almond, David; Cardozo, Timothy

    2010-01-01

    The antigenic diversity of HIV-1 has long been an obstacle to vaccine design, and this variability is especially pronounced in the V3 loop of the virus' surface envelope glycoprotein. We previously proposed that the crown of the V3 loop, although dynamic and sequence variable, is constrained throughout the population of HIV-1 viruses to an immunologically relevant β-hairpin tertiary structure. Importantly, there are thousands of different V3 loop crown sequences in circulating HIV-1 viruses, making 3D structural characterization of trends across the diversity of viruses difficult or impossible by crystallography or NMR. Our previous successful studies with folding of the V3 crown1, 2 used the ab initio algorithm 3 accessible in the ICM-Pro molecular modeling software package (Molsoft LLC, La Jolla, CA) and suggested that the crown of the V3 loop, specifically from positions 10 to 22, benefits sufficiently from the flexibility and length of its flanking stems to behave to a large degree as if it were an unconstrained peptide freely folding in solution. As such, rapid ab initio folding of just this portion of the V3 loop of any individual strain of the 60,000+ circulating HIV-1 strains can be informative. Here, we folded the V3 loop of the R2 strain to gain insight into the structural basis of its unique properties. R2 bears a rare V3 loop sequence thought to be responsible for the exquisite sensitivity of this strain to neutralization by patient sera and monoclonal antibodies4, 5. The strain mediates CD4-independent infection and appears to elicit broadly neutralizing antibodies. We demonstrate how evaluation of the results of the folding can be informative for associating observed structures in the folding with the immunological activities observed for R2. PMID:20864931

  11. Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold

    PubMed Central

    Totrov, Maxim; Jiang, Xunqing; Kong, Xiang-Peng; Cohen, Sandra; Krachmarov, Chavdar; Williams, Constance; Seaman, Michael S.; Cardozo, Timothy; Gorny, Miroslaw K; Wang, Shixia; Lu, Shan; Pinter, Abraham; Zolla-Pazner, Susan

    2010-01-01

    V3 loop is a major neutralizing determinant of the HIV-1 gp120. Using 3D structures of cholera toxin B subunit (CTB), complete V3 in the gp120 context and V3 bound to a monoclonal antibody (mAb) we designed two V3-scaffold immunogen constructs (V3-CTB). The full-length V3-CTB presenting the complete V3 in a structural context mimicking gp120, was recognized by the large majority of our panel of 24 mAbs. The short V3-CTB presenting a V3 fragment in the conformation observed in the complex with the 447-52D Fab, exhibited high affinity binding to this mAb. The immunogens were evaluated in rabbits using DNA-prime/protein-boost protocol. Boosting with the full-length V3-CTB induced high anti-V3 titers in sera that potently neutralize multiple HIV virus strains. The short V3-CTB was ineffective. The results suggest that very narrow antigenic profile of an immunogen is associated with poor Ab response. An immunogen with broader antigenic activity elicits robust Ab response. PMID:20663531

  12. Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.

    PubMed

    Totrov, Maxim; Jiang, Xunqing; Kong, Xiang-Peng; Cohen, Sandra; Krachmarov, Chavdar; Salomon, Aidy; Williams, Constance; Seaman, Michael S; Abagyan, Ruben; Cardozo, Timothy; Gorny, Miroslaw K; Wang, Shixia; Lu, Shan; Pinter, Abraham; Zolla-Pazner, Susan

    2010-09-30

    V3 loop is a major neutralizing determinant of the HIV-1 gp120. Using 3D structures of cholera toxin B subunit (CTB), complete V3 in the gp120 context, and V3 bound to a monoclonal antibody (mAb), we designed two V3-scaffold immunogen constructs (V3-CTB). The full-length V3-CTB presenting the complete V3 in a structural context mimicking gp120 was recognized by the large majority of our panel of 24 mAbs. The short V3-CTB presenting a V3 fragment in the conformation observed in the complex with the 447-52D Fab, exhibited high-affinity binding to this mAb. The immunogens were evaluated in rabbits using DNA-prime/protein-boost protocol. Boosting with the full-length V3-CTB induced high anti-V3 titers in sera that potently neutralize multiple HIV virus strains. The short V3-CTB was ineffective. The results suggest that very narrow antigenic profile of an immunogen is associated with poor Ab response. An immunogen with broader antigenic activity elicits robust Ab response. PMID:20663531

  13. Structure-guided Design and Immunological Characterization of Immunogens Presenting the HIV-1 gp120 V3 Loop on a CTB Scaffold

    SciTech Connect

    M Totrov; X Jiang; X Kong; S Cohen; C Krachmarov; A Salomon; C Williams; M Seaman; R Abagyan; et al.

    2011-12-31

    V3 loop is a major neutralizing determinant of the HIV-1 gp120. Using 3D structures of cholera toxin B subunit (CTB), complete V3 in the gp120 context, and V3 bound to a monoclonal antibody (mAb), we designed two V3-scaffold immunogen constructs (V3-CTB). The full-length V3-CTB presenting the complete V3 in a structural context mimicking gp120 was recognized by the large majority of our panel of 24 mAbs. The short V3-CTB presenting a V3 fragment in the conformation observed in the complex with the 447-52D Fab, exhibited high-affinity binding to this mAb. The immunogens were evaluated in rabbits using DNA-prime/protein-boost protocol. Boosting with the full-length V3-CTB induced high anti-V3 titers in sera that potently neutralize multiple HIV virus strains. The short V3-CTB was ineffective. The results suggest that very narrow antigenic profile of an immunogen is associated with poor Ab response. An immunogen with broader antigenic activity elicits robust Ab response.

  14. Structural differences within the loop E motif imply alternative mechanisms of viroid processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Viroids replicate via a rolling circle mechanism, and cleavage/ligation requires extensive rearrangement of the highly base-paired native structure. For Potato spindle tuber viroid (PSTVd), the switch from cleavage to ligation is driven by the change from a multi-branched tetraloop structure to a l...

  15. Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface.

    PubMed

    Franklin, Matthew C; Rudolph, Michael J; Ginter, Christopher; Cassidy, Michael S; Cheung, Jonah

    2016-09-01

    Irreversible inhibition of the essential nervous system enzyme acetylcholinesterase by organophosphate nerve agents and pesticides may quickly lead to death. Oxime reactivators currently used as antidotes are generally less effective against pesticide exposure than nerve agent exposure, and pesticide exposure constitutes the majority of cases of organophosphate poisoning in the world. The current lack of published structural data specific to human acetylcholinesterase organophosphate-inhibited and oxime-bound states hinders development of effective medical treatments. We have solved structures of human acetylcholinesterase in different states in complex with the organophosphate insecticide, paraoxon, and oximes. Reaction with paraoxon results in a highly perturbed acyl loop that causes a narrowing of the gorge in the peripheral site that may impede entry of reactivators. This appears characteristic of acetylcholinesterase inhibition by organophosphate insecticides but not nerve agents. Additional changes seen at the dimer interface are novel and provide further examples of the disruptive effect of paraoxon. Ternary structures of paraoxon-inhibited human acetylcholinesterase in complex with the oximes HI6 and 2-PAM reveals relatively poor positioning for reactivation. This study provides a structural foundation for improved reactivator design for the treatment of organophosphate intoxication. Proteins 2016; 84:1246-1256. © 2016 Wiley Periodicals, Inc. PMID:27191504

  16. Investigation of Deterioration Behavior of Hysteretic Loops in Nonlinear Static Procedure Analysis of Concrete Structures with Shear Walls

    SciTech Connect

    Ghodrati Amiri, G.; Amidi, S.; Khorasani, M.

    2008-07-08

    In the recent years, scientists developed the seismic rehabilitation of structures and their view points were changed from sufficient strength to the performance of structures (Performance Base Design) to prepare a safe design. Nonlinear Static Procedure analysis (NSP) or pushover analysis is a new method that is chosen for its speed and simplicity in calculations. 'Seismic Rehabilitation Code for Existing Buildings' and FEMA 356 considered this method. Result of this analysis is a target displacement that is the base of the performance and rehabilitation procedure of the structures. Exact recognition of that displacement could develop the workability of pushover analysis. In these days, Nonlinear Dynamic Analysis (NDP) is only method can exactly apply the seismic ground motions. In this case because it consumes time, costs very high and is more difficult than other methods, is not applicable as much as NSP. A coefficient used in NSP for determining the target displacement is C2 (Stiffness and Strength Degradations Coefficient) and is applicable for correcting the errors due to eliminating the stiffness and strength degradations in hysteretic loops. In this study it has been tried to analysis three concrete frames with shear walls by several accelerations that scaled according to FEMA 273 and FEMA 356. These structures were designed with Iranian 2800 standard (vers.3). Finally after the analyzing by pushover method and comparison results with dynamic analysis, calculated C2 was comprised with values in rehabilitation codes.

  17. Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

    PubMed Central

    Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

    2015-01-01

    Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

  18. Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer

    NASA Astrophysics Data System (ADS)

    Lewis, Mitchell; Chang, Geoffrey; Horton, Nancy C.; Kercher, Michele A.; Pace, Helen C.; Schumacher, Maria A.; Brennan, Richard G.; Lu, Ponzy

    1996-03-01

    The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-β-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.

  19. The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120.

    PubMed

    Karasavvas, Nicos; Billings, Erik; Rao, Mangala; Williams, Constance; Zolla-Pazner, Susan; Bailer, Robert T; Koup, Richard A; Madnote, Sirinan; Arworn, Duangnapa; Shen, Xiaoying; Tomaras, Georgia D; Currier, Jeffrey R; Jiang, Mike; Magaret, Craig; Andrews, Charla; Gottardo, Raphael; Gilbert, Peter; Cardozo, Timothy J; Rerks-Ngarm, Supachai; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Paris, Robert; Greene, Kelli; Gao, Hongmei; Gurunathan, Sanjay; Tartaglia, Jim; Sinangil, Faruk; Korber, Bette T; Montefiori, David C; Mascola, John R; Robb, Merlin L; Haynes, Barton F; Ngauy, Viseth; Michael, Nelson L; Kim, Jerome H; de Souza, Mark S

    2012-11-01

    The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200-3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100-200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169-184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100-800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100-3200) and 3570 (range: 200-12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition.

  20. Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine

    PubMed Central

    Nys, Mieke; Wijckmans, Eveline; Farinha, Ana; Yoluk, Özge; Andersson, Magnus; Brams, Marijke; Spurny, Radovan; Peigneur, Steve; Tytgat, Jan; Lindahl, Erik; Ulens, Chris

    2016-01-01

    Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor. In this study, we determine the molecular determinants of chlorpromazine binding in the Erwinia ligand-gated ion channel (ELIC). We report the X-ray crystal structures of ELIC in complex with chlorpromazine or its brominated derivative bromopromazine. Unexpectedly, we do not find a chlorpromazine molecule in the channel pore of ELIC, but behind the β8–β9 loop in the extracellular ligand-binding domain. The β8–β9 loop is localized downstream from the neurotransmitter binding site and plays an important role in coupling of ligand binding to channel opening. In combination with electrophysiological recordings from ELIC cysteine mutants and a thiol-reactive derivative of chlorpromazine, we demonstrate that chlorpromazine binding at the β8–β9 loop is responsible for receptor inhibition. We further use molecular-dynamics simulations to support the X-ray data and mutagenesis experiments. Together, these data unveil an allosteric binding site in the extracellular ligand-binding domain of ELIC. Our results extend on previous observations and further substantiate our understanding of a multisite model for allosteric modulation of Cys-loop receptors. PMID:27791038

  1. Defect Induced Electronic Structure of Uranofullerene

    PubMed Central

    Dai, Xing; Cheng, Cheng; Zhang, Wei; Xin, Minsi; Huai, Ping; Zhang, Ruiqin; Wang, Zhigang

    2013-01-01

    The interaction between the inner atoms/cluster and the outer fullerene cage is the source of various novel properties of endohedral metallofullerenes. Herein, we introduce an adatom-type spin polarization defect on the surface of a typical endohedral stable U2@C60 to predict the associated structure and electronic properties of U2@C61 based on the density functional theory method. We found that defect induces obvious changes in the electronic structure of this metallofullerene. More interestingly, the ground state of U2@C61 is nonet spin in contrast to the septet of U2@C60. Electronic structure analysis shows that the inner U atoms and the C ad-atom on the surface of the cage contribute together to this spin state, which is brought about by a ferromagnetic coupling between the spin of the unpaired electrons of the U atoms and the C ad-atom. This discovery may provide a possible approach to adapt the electronic structure properties of endohedral metallofullerenes. PMID:23439318

  2. Utilising a loop structure to allow a microfiber coupler with larger taper diameters to be used for sensing

    NASA Astrophysics Data System (ADS)

    Wei, Fangfang; Farrell, Gerald; Wu, Qiang; Semenova, Yuliya

    2016-05-01

    This paper examines a technique that utilizes a Sagnac loop with a microfiber coupler (MFC) as a coupler which allows the MFC to operate effectively as a sensor but with larger than normal tapered fiber diameters. The proposed structure is found to be suitable for temperature and refractive index (RI) sensing. It is shown that a variation in the surrounding of the MFC RI results in a shift of the output spectrum, while a temperature variation leads to changes in the intensity of the interference dips. A decrease in the waist diameter of the MFC results in an increase in the sensitivity to temperature. For MFC structures based on a 5.6 μm and a 3 μm fiber waist diameter, the minimum transmission power level of a selected spectral dip decreases by 1.7 dB and 5.03 dB respectively, as the temperature changes from 18 °C to 44 °C. A change in the surrounding RI from 1.334 to 1.395 results in the spectral redshift of 8 nm using a 5.6 μm fiber waist diameter. By functionalizing the surface of the MFC with various materials, the structure could potentially be used for sensing of other parameters.

  3. Coronal Density Structure and its Role in Wave Damping in Loops

    NASA Astrophysics Data System (ADS)

    Cargill, P. J.; De Moortel, I.; Kiddie, G.

    2016-05-01

    It has long been established that gradients in the Alfvén speed, and in particular the plasma density, are an essential part of the damping of waves in the magnetically closed solar corona by mechanisms such as resonant absorption and phase mixing. While models of wave damping often assume a fixed density gradient, in this paper the self-consistency of such calculations is assessed by examining the temporal evolution of the coronal density. It is shown conceptually that for some coronal structures, density gradients can evolve in a way that the wave-damping processes are inhibited. For the case of phase mixing we argue that (a) wave heating cannot sustain the assumed density structure and (b) inclusion of feedback of the heating on the density gradient can lead to a highly structured density, although on long timescales. In addition, transport coefficients well in excess of classical are required to maintain the observed coronal density. Hence, the heating of closed coronal structures by global oscillations may face problems arising from the assumption of a fixed density gradient, and the rapid damping of oscillations may have to be accompanied by a separate (non-wave-based) heating mechanism to sustain the required density structuring.

  4. Structures induced by companions in galactic discs

    NASA Astrophysics Data System (ADS)

    Kyziropoulos, P. E.; Efthymiopoulos, C.; Gravvanis, G. A.; Patsis, P. A.

    2016-09-01

    Using N-body simulations we study the structures induced on a galactic disc by repeated flybys of a companion in decaying eccentric orbit around the disc. Our system is composed by a stellar disc, bulge and live dark matter halo, and we study the system's dynamical response to a sequence of a companion's flybys, when we vary i) the disc's temperature (parameterized by Toomre's Q-parameter) and ii) the companion's mass and initial orbit. We use a new 3D Cartesian grid code: MAIN (Mesh-adaptive Approximate Inverse N-body solver). The main features of MAIN are reviewed, with emphasis on the use of a new Symmetric Factored Approximate Sparse Inverse (SFASI) matrix in conjunction with the multigrid method that allows the efficient solution of Poisson's equation in three space variables. We find that: i) companions need to be assigned initial masses in a rather narrow window of values in order to produce significant and more long-standing non-axisymmetric structures (bars and spirals) in the main galaxy's disc by the repeated flyby mechanism. ii) a crucial phenomenon is the antagonism between companion-excited and self-excited modes on the disc. Values of Q > 1.5 are needed in order to allow for the growth of the companion-excited modes to prevail over the the growth of the disc's self-excited modes. iii) We give evidence that the companion-induced spiral structure is best represented by a density wave with pattern speed nearly constant in a region extending from the ILR to a radius close to, but inside, corotation.

  5. Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5′-end stem-loop structures

    PubMed Central

    Li, You; Ho, Eric S.; Gunderson, Samuel I.; Kiledjian, Megerditch

    2009-01-01

    mRNA decapping is a critical step in the control of mRNA stability and gene expression and is carried out by the Dcp2 protein. Dcp2 is an RNA-binding protein that must bind the RNA in order to recognize the cap for hydrolysis. We previously demonstrated that a 60 nucleotide (nt) element at the 5′ end of the mRNA encoding Rrp41 is preferentially bound and decapped by Dcp2. Here, we demonstrate that enhanced decapping of this element is dependent on the structural integrity of its first 33 nt and not its primary sequence. The structure consists of a stem-loop positioned <10 nt from the 5′ end of the mRNA. The generality of a stem-loop structure in enhanced Dcp2-mediated decapping was underscored by the identification of additional potential Dcp2 substrate mRNAs by a global analysis of human mRNAs containing a similar predicted stem-loop structure at their respective 5′ end. These studies suggest a general role for 5′ stem-loops in enhancing decapping activity and the utilization of this structure as a predictive tool for Dcp2 target substrates. These studies also demonstrate that Dcp2 alone in the absence of additional proteins can preferentially associate with and modulate mRNA decapping. PMID:19233875

  6. Loop-Closure and Gaussian Models of Collective Structural Characteristics of Capped PEO Oligomers in Water.

    PubMed

    Chaudhari, M I; Pratt, L R; Paulaitis, M E

    2015-07-23

    Parallel-tempering MD results for a CH3(CH2-O-CH2)mCH3 chain in water are exploited as a database for analysis of collective structural characteristics of the PEO globule with a goal of defining models permitting statistical thermodynamic analysis of dispersants of Corexit type. The chain structure factor, relevant to neutron scattering from a deuterated chain in null water, is considered specifically. The traditional continuum-Gaussian structure factor is inconsistent with the simple k → ∞ behavior, but we consider a discrete-Gaussian model that does achieve that consistency. Shifting and scaling the discrete-Gaussian model helps to identify the low-k to high-k transition near k ≈ 2π/0.6 nm when an empirically matched number of Gaussian links is about one-third of the total number of effective atom sites. This short distance-scale boundary of 0.6 nm is directly verified with the r space distributions, and this distance is thus identified with a natural size for coarsened monomers. The probability distribution of Rg(2) is compared with the classic predictions for both the Gaussian model and freely jointed chains. ⟨Rg(2)(j)⟩, the contribution of the jth chain segment to ⟨Rg(2)⟩, depends on the contour index about as expected for Gaussian chains despite significant quantitative discrepancies that express the swelling of these chains in water. Monomers central to the chain contour occupy the center of the chain globule. The density profiles of chain segments relative to their center of mass can show distinctive density structuring for smaller chains due to the close proximity of central elements to the globule center. However, that density structuring washes out for longer chains where many chain elements additively contribute to the density profiles. Gaussian chain models thus become more satisfactory for the density profiles for longer chains. PMID:25121580

  7. Magnetic loops, downflows, and convection in the solar corona

    NASA Technical Reports Server (NTRS)

    Foukal, P.

    1978-01-01

    Optical and extreme-ultraviolet observations of solar loop structures show that flows of cool plasma from condensations near the loop apex are a common property of loops associated with radiations whose maximum temperature is greater than approximately 7000 K and less than approximately 3,000,000 K. It is suggested that the mass balance of these structures indicates reconnection by means of plasma motion across field lines under rather general circumstances (not only after flares). It is shown that the cool material has lower gas pressure than the surrounding coronal medium. The density structure of the bright extreme ultraviolet loops suggests that downflows of cool gas result from isobaric condensation of plasma that is either out of thermal equilibrium with the local energy deposition rate into the corona, or is thermally unstable. The evidence is thought to indicate that magnetic fields act to induce a pattern of forced convection.

  8. Large-scale structure from cosmic-string loops in a baryon-dominated universe

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Scherrer, Robert J.

    1988-01-01

    The results are presented of a numerical simulation of the formation of large-scale structure in a universe with Omega(0) = 0.2 and h = 0.5 dominated by baryons in which cosmic strings provide the initial density perturbations. The numerical model yields a power spectrum. Nonlinear evolution confirms that the model can account for 700 km/s bulk flows and a strong cluster-cluster correlation, but does rather poorly on smaller scales. There is no visual 'filamentary' structure, and the two-point correlation has too steep a logarithmic slope. The value of G mu = 4 x 10 to the -6th is significantly lower than previous estimates for the value of G mu in baryon-dominated cosmic string models.

  9. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    PubMed Central

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-01-01

    Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P21 with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P21 crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-­barrel and (iii) in the extended C-terminal segment, which is attached to the β-­barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family. PMID:19770509

  10. Assembly induced delaminations in composite structures

    NASA Technical Reports Server (NTRS)

    Goering, J.; Bohlmann, R.; Wanthal, S.; Kautz, E.; Neri, Lawrence M.

    1992-01-01

    Experimental and analytical studies of the development of delaminations around fastener holes in composite structures are presented. This type of delamination is known to occur in composite skins that are mechanically fastened to a poorly mating substructure. Results of an experimental study to determine the resistance of laminates to the initiation of assembly induced delaminations and the residual strength of assembly damaged coupons are presented for AS4/3501-6, IM7/8551-7A, and AS4/PEEK material systems. A survey of existing analytical models for predicting the residual strength and stability of delaminations is presented, and the development of a new model for predicting the initiation of delaminations around a fastener hole is outlined. The fastener hole damage initiation model utilizes a finite element based Fourier series solution, and is validated through comparisons of analytical and experimental results.

  11. Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

    SciTech Connect

    Brandao, T.; Robinson, H; Johnson, S; Hengge, A

    2009-01-01

    Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.

  12. R-loop-mediated genomic instability is caused by impairment of replication fork progression.

    PubMed

    Gan, Wenjian; Guan, Zhishuang; Liu, Jie; Gui, Ting; Shen, Keng; Manley, James L; Li, Xialu

    2011-10-01

    Transcriptional R loops are anomalous RNA:DNA hybrids that have been detected in organisms from bacteria to humans. These structures have been shown in eukaryotes to result in DNA damage and rearrangements; however, the mechanisms underlying these effects have remained largely unknown. To investigate this, we first show that R-loop formation induces chromosomal DNA rearrangements and recombination in Escherichia coli, just as it does in eukaryotes. More importantly, we then show that R-loop formation causes DNA replication fork stalling, and that this in fact underlies the effects of R loops on genomic stability. Strikingly, we found that attenuation of replication strongly suppresses R-loop-mediated DNA rearrangements in both E. coli and HeLa cells. Our findings thus provide a direct demonstration that R-loop formation impairs DNA replication and that this is responsible for the deleterious effects of R loops on genome stability from bacteria to humans.

  13. NMR structure of the noncytotoxic α-sarcin mutant Δ(7-22): The importance of the native conformation of peripheral loops for activity

    PubMed Central

    García-Mayoral, Ma Flor; García-Ortega, Lucia; Lillo, Ma Pilar; Santoro, Jorge; Martínez Del Pozo, Álvaro; Gavilanes, José G.; Rico, Manuel; Bruix, Marta

    2004-01-01

    The deletion mutant Δ(7-22) of α-sarcin, unlike its wild-type protein counterpart, lacks the specific ability to degrade rRNA in intact ribosomes and exhibits an increased unspecific ribonuclease activity and decreased interaction with lipid vesicles. In trying to shed light on these differences, we report here on the three-dimensional structure of the Δ(7-22) α-sarcin mutant using NMR methods. We also evaluated its dynamic properties on the basis of theoretical models and measured its correlation time (6.2 nsec) by time-resolved fluorescence anisotropy. The global fold characteristic of ribotoxins is preserved in the mutant. The most significant differences with respect to the α-sarcin structure are concentrated in (1) loop 2, (2) loop 3, which adopts a new orientation, and (3) loop 5, which shows multiple conformations and an altered dynamics. The interactions between loop 5 and the N-terminal hairpin are lost in the mutant, producing increased solvent accessibility of the active-site residues. The degree of solvent exposure of the catalytic His 137 is similar to that shown by His 92 in RNase T1. Additionally, the calculated order parameters of residues belonging to loop 5 in the mutant correspond to an internal dynamic behavior more similar to RNase T1 than α-sarcin. On the other hand, changes in the relative orientation of loop 3 move the lysine-rich region 111–114, crucial for substrate recognition, away from the active site. All of the structural and dynamic data presented here reveal that the mutant is a hybrid of ribotoxins and noncytotoxic ribonucleases, consistent with its biological properties. PMID:15044731

  14. Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis.

    PubMed

    Edink, Ewald; Rucktooa, Prakash; Retra, Kim; Akdemir, Atilla; Nahar, Tariq; Zuiderveld, Obbe; van Elk, René; Janssen, Elwin; van Nierop, Pim; van Muijlwijk-Koezen, Jacqueline; Smit, August B; Sixma, Titia K; Leurs, Rob; de Esch, Iwan J P

    2011-04-13

    Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches. PMID:21322593

  15. Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination.

    PubMed

    Draghici, Heidrun-Katharina; Varrelmann, Mark

    2010-02-01

    Virus RNA recombination, one of the main factors for genetic variability and evolution, is thought to be based on different mechanisms. Here, the recently described in vivo potato virus X (PVX) recombination assay [Draghici, H.-K. & Varrelmann, M. (2009). J Virol 83, 7761-7769] was applied to characterize structural parameters of recombination. The assay uses an Agrobacterium-mediated expression system incorporating a PVX green fluorescent protein (GFP)-labelled full-length clone. The clone contains a partial coat protein (CP) deletion that causes defectiveness in cell-to-cell movement, together with a functional CP+3' non-translated region (ntr) transcript, in Nicotiana benthamiana leaf tissue. The structural parameters assessed were the length of sequence overlap, the distance between mutations and the degree of sequence similarity. The effects on the observed frequency of reconstitution and the composition of the recombination products were characterized. Application of four different type X intact PVX CP genes with variable composition allowed the estimation of the junction sites of precise homologous recombination. Although one template switch would have been sufficient for functional reconstitution, between one and seven template switches were observed. Use of PVX-GFP mutants with CP deletions of variable length resulted in a linear decrease of the reconstitution frequency. The critical length observed for homologous recombination was 20-50 nt. Reduction of the reconstitution frequency was obtained when a phylogenetically distant PVX type Bi CP gene was used. Finally, the prediction of CP and 3'-ntr RNA secondary structure demonstrated that recombination-junction sites were located mainly in regions of stem-loop structures, allowing the recombination observed to be categorized as similarity-assisted.

  16. Determinants of RNA hairpin loop-loop complex stability.

    PubMed

    Gregorian, R S; Crothers, D M

    1995-05-19

    Complexes formed by RNA hairpin loops with complementary loop sequences derived from Escherichia coli RNA I and RNA II, which are involved in the control of DNA replication of plasmid ColE1, have been analyzed to determine the sequence and structural elements required to achieve full affinity. Of particular interest is the origin of the enhanced stability of the complex formed by hairpin loops whose loop sequences have been inverted 5' to 3' with respect to wild-type sequences. Full complementarity of the two interacting loops is required to achieve full or enhanced affinity, while the stems of the two hairpins can differ. The major determinant of enhanced affinity lies in the base-pairs formed at positions 1 and 7 of the loops, together with the two base-pairs of each stem which are closest to the loop. Sequence variation in the middle of the loops, or further down the stem away from the loops, exerts only a modest influence on complex stability. We incorporate these results into a model for the loop-loop interaction which accounts for the importance of positions one and seven and the first two nucleotides of the stem, while providing potentially unique structures for recognition by the RNA one modulator protein. PMID:7539081

  17. Determinants of RNA hairpin loop-loop complex stability.

    PubMed

    Gregorian, R S; Crothers, D M

    1995-05-19

    Complexes formed by RNA hairpin loops with complementary loop sequences derived from Escherichia coli RNA I and RNA II, which are involved in the control of DNA replication of plasmid ColE1, have been analyzed to determine the sequence and structural elements required to achieve full affinity. Of particular interest is the origin of the enhanced stability of the complex formed by hairpin loops whose loop sequences have been inverted 5' to 3' with respect to wild-type sequences. Full complementarity of the two interacting loops is required to achieve full or enhanced affinity, while the stems of the two hairpins can differ. The major determinant of enhanced affinity lies in the base-pairs formed at positions 1 and 7 of the loops, together with the two base-pairs of each stem which are closest to the loop. Sequence variation in the middle of the loops, or further down the stem away from the loops, exerts only a modest influence on complex stability. We incorporate these results into a model for the loop-loop interaction which accounts for the importance of positions one and seven and the first two nucleotides of the stem, while providing potentially unique structures for recognition by the RNA one modulator protein.

  18. Effects of Flow on Structure and Abundances in Multispecies Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Lenz, Dawn D.

    2004-03-01

    We investigate the effects of large-scale bulk flows on coronal abundances using a multispecies numerical model. The model assumes that electrons, protons, and helium are in thermal equilibrium and constitute the bulk of the coronal plasma. Thermal diffusion and Coulomb friction are included. Temperature profiles for the bulk component and for each ion species are assumed, so the model reduces to a solution of mass and force balance for each component. We further assume that the bulk component has an upward bulk velocity at the base, and that ion flow speeds along field lines are negligible relative to the bulk flow. Coulomb coupling of the electrons and ions induces drag that counteracts the tendency of the ions to gravitationally settle. In regions of small ∇T, such as the outer regions of the corona, Coulomb drag is the only significant force counteracting gravitational settling in this model. We find that relatively modest bulk flows of tens of km s-1 can enhance ion abundances by 2-3 orders of magnitude over their values in low- or no-flow cases.

  19. Performance Comparison of BPL, EtherLoop and SHDSL technology performance on existing pilot cable circuits under the presence of induced voltage

    NASA Astrophysics Data System (ADS)

    Che, Y. X.; Ong, H. S.; Lai, L. C.; Karuppiah, S.; Ong, X. J.; Do, N. Q.

    2013-06-01

    Pilot cable is originally used for utility protection. Then, pilot cable is further utilized for SCADA communication with low frequency PSK modem in the early 1990. However, the quality of pilot cable communication drops recently. Pilot cable starts to deteriorate due to aging and other unknown factors. It is also believed that the presence of induced voltage causes interference to existing modem communication which operates at low frequency channel. Therefore, BPL (Broadband Power Line), EtherLoop and SHDSL (Symmetrical High-speed Digital Subscriber Line) modem technology are proposed as alternative communication solutions for pilot cable communication. The performance of the 3 selected technologies on existing pilot cable circuits under the presence of induced voltage are measured and compared. Total of 11 pilot circuits with different length and level of induced voltage influence are selected for modem testing. The performance of BPL, EtherLoop and SHDSL modem technology are measured by the delay, bandwidth, packet loss and the long term usability SCADA (Supervisory Control and Data Acquisition) application. The testing results are presented and discussed in this paper. The results show that the 3 selected technologies are dependent on distance and independent on the level of induced voltage.

  20. A Structured Loop Modulates Coupling between the Substrate-binding and Dimerization Domains in the Multidrug Resistance Transporter EmrE*

    PubMed Central

    Banigan, James R.; Gayen, Anindita; Cho, Min-Kyu; Traaseth, Nathaniel J.

    2015-01-01

    Secondary active transporters undergo large conformational changes to facilitate the efflux of substrates across the lipid bilayer. Among the smallest known transport proteins are members of the small multidrug resistance (SMR) family that are composed of four transmembrane (TM) domains and assemble into dimers. An unanswered question in the SMR field is how the dimerization domain (TM4) is coupled with the substrate-binding chamber (TM1–3). To provide insight for this essential aspect of ion-coupled transport, we carried out a structure-function study on the SMR protein EmrE using solid-state NMR spectroscopy in lipid bilayers and resistance assays in Escherichia coli. The chemical shifts for EmrE were consistent with β-strand secondary structure for the loop connecting TM3 and TM4. Based on these structural results, EmrE mutants were created to ascertain whether a specific loop length and composition were necessary for function. A linker encompassing six extra Gly residues relative to wild-type EmrE failed to give resistance; however, the number of residues in the loop was not the only criterion for a functional efflux pump. Replacement of the central hydrophobic residue with Gly (L83G) also conferred no ethidium resistance phenotype, which supported the conclusion that the structure and length of the loop were both essential for ion-coupled transport. Taken together with a bioinformatics analysis, a structured linker is likely conserved across the SMR family to play an active role in mediating the conformational switch between inward-open and outward-open states necessary for drug efflux. These findings underscore the important role loops can play in mediating efflux. PMID:25406320

  1. Determining the invariant structure elements of the HIV-1 variable V3 loops: insight into the HIV-MN and HIV-Haiti isolates.

    PubMed

    Andrianov, Alexander M

    2008-10-01

    The computer approaches that combined the 3D protein structure modeling with the mathematical statistics methods were used to compute the NMR-based 3D structures of the HIV-1 gp120 V3 loop for the HIV-MN and HIV-Haiti isolates in water as well as to compare their conformational characteristics with the purpose of determining the structure elements common for the two virus modifications. As a result, the variability of the amino acid sequence was found to stimulate the considerable structural rearrangements of the V3 loop. However, despite this fact, one functionally crucial stretch of V3 and a greater portion of its residues were shown to preserve the conformations in the viral strains of interest. To reveal the structural motifs and individual amino acids giving rise to the close conformations in the HIV-MN and HIV-Haiti V3 loops regardless of the sequence and environment variability, the simulated structures were collated with those deciphered previously in terms of NMR data in a water/trifluoroethanol mixed solvent. The structure elements and single residues of V3 residing in its biologically significant sites and keeping the conformations in all of the cases at question are considered to be the promising targets for anti-AIDS drugs studies. In this context, the structurally inflexible motifs of V3 presenting the weak units in the virus protection system may be utilized as the most convenient landing-places for molecular docking of the V3 loop and ligand structures followed by selecting chemical compounds suitable as a basis for the design of safe and effective antiviral agents. PMID:18597546

  2. Natively Unstructured Loops Differ from Other Loops

    PubMed Central

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-01-01

    Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%–70% of all worm proteins observed to have more than seven protein–protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long

  3. Natively unstructured loops differ from other loops.

    PubMed

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-07-01

    Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long

  4. Ternary complex structure of human HGPRTase, PRPP, Mg2+, and the inhibitor HPP reveals the involvement of the flexible loop in substrate binding.

    PubMed Central

    Balendiran, G. K.; Molina, J. A.; Xu, Y.; Torres-Martinez, J.; Stevens, R.; Focia, P. J.; Eakin, A. E.; Sacchettini, J. C.; Craig, S. P.

    1999-01-01

    Site-directed mutagenesis was used to replace Lys68 of the human hypoxanthine phosphoribosyltransferase (HGPRTase) with alanine to exploit this less reactive form of the enzyme to gain additional insights into the structure activity relationship of HGPRTase. Although this substitution resulted in only a minimal (one- to threefold) increase in the Km values for binding pyrophosphate or phosphoribosylpyrophosphate, the catalytic efficiencies (k(cat)/Km) of the forward and reverse reactions were more severely reduced (6- to 30-fold), and the mutant enzyme showed positive cooperativity in binding of alpha-D-5-phosphoribosyl-1-pyrophosphate (PRPP) and nucleotide. The K68A form of the human HGPRTase was cocrystallized with 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and Mg PRPP, and the refined structure reported. The PRPP molecule built into the [(Fo - Fc)phi(calc)] electron density shows atomic interactions between the Mg PRPP and enzyme residues in the pyrophosphate binding domain as well as in a long flexible loop (residues Leu101 to Gly111) that closes over the active site. Loop closure reveals the functional roles for the conserved SY dipeptide of the loop as well as the molecular basis for one form of gouty arthritis (S103R). In addition, the closed loop conformation provides structural information relevant to the mechanism of catalysis in human HGPRTase. PMID:10338013

  5. Rectified Continuous Flow Loop for the Thermal Management of Large Structures

    NASA Astrophysics Data System (ADS)

    Skye, H. M.; Hoch, D. W.; Nellis, G. F.; Maddocks, J. R.; Klein, S. A.; Roberts, T.; Davis, T.

    2006-04-01

    Distributed loads are frequently encountered in large deployable structures used in space applications such as optical mirrors, actively cooled sunshades, and on focal plane electronics. One mechanism for providing distributed cooling is via an oscillatory cryocooler such as a pulse-tube that is integrated with a fluid rectification system consisting of check-valves and buffer volumes in order to extract a small amount of continuous flow. This continuous flow allows relatively large loads to be accepted over a long distance with a small temperature difference and has advantages relative to vibration and electrical isolation. Also, it is possible to provide rapid and precise temperature control via modulation of the flow rate. The same working fluid, helium, can be used throughout the entire system, reducing complexity and simplifying the contamination control process. This paper describes steady state and transient modeling results and presents experimental data for a single-stage pulse tube with a rectifying interface that is integrated with a distributed load. The predicted and measured steady state and transient behaviors are compared. The experimental data are used to demonstrate the thermal management concept and illustrate how it can be used for rapid and precise temperature control.

  6. On the environmental decoherence and spin interference in mesoscopic loop structures

    NASA Astrophysics Data System (ADS)

    Tralle, I.; Paśko, W.

    2003-09-01

    Mechanisms of ‘environmental decoherence’ such as surface scattering, Elliot-Yafet process and precession mechanisms, as well as their influence on the spin phase relaxation are considered and compared. It is shown that the ‘spin ballistic’ regime is possible, when the phase relaxation length for the spin part of the wave function ( Lϕ(s)) is much greater than the phase relaxation length for the ‘orbital part’ ( Lϕ(e)). In the presence of an additional magnetic field, the spin part of the electron's wave function (WF) acquires a phase shift due to additional spin precession about that field. If the structure length L is chosen to be Lϕ(s)> L> Lϕ(e), it is possible to ‘wash out’ the quantum interference related to the phase coherence of the ‘orbital part’ of the WF, retaining at the same time that related to the phase coherence of the spin part and, hence, to reveal corresponding conductance oscillations.

  7. Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold with a Characteristic Inhibitory Loop*

    PubMed Central

    Arai, Ryoichi; Fukui, Sadaharu; Kobayashi, Naoya; Sekiguchi, Junichi

    2012-01-01

    In Bacillus subtilis, LytE, LytF, CwlS, and CwlO are vegetative autolysins, dl-endopeptidases in the NlpC/P60 family, and play essential roles in cell growth and separation. IseA (YoeB) is a proteinaceous inhibitor against the dl-endopeptidases, peptidoglycan hydrolases. Overexpression of IseA caused significantly long chained cell morphology, because IseA inhibits the cell separation dl-endopeptidases post-translationally. Here, we report the first three-dimensional structure of IseA, determined by NMR spectroscopy. The structure includes a single domain consisting of three α-helices, one 310-helix, and eight β-strands, which is a novel fold like a “hacksaw.” Noteworthy is a dynamic loop between β4 and the 310-helix, which resembles a “blade.” The electrostatic potential distribution shows that most of the surface is positively charged, but the region around the loop is negatively charged. In contrast, the LytF active-site cleft is expected to be positively charged. NMR chemical shift perturbation of IseA interacting with LytF indicated that potential interaction sites are located around the loop. Furthermore, the IseA mutants D100K/D102K and G99P/G101P at the loop showed dramatic loss of inhibition activity against LytF, compared with wild-type IseA, indicating that the β4–310 loop plays an important role in inhibition. Moreover, we built a complex structure model of IseA-LytF by docking simulation, suggesting that the β4–310 loop of IseA gets stuck deep in the cleft of LytF, and the active site is occluded. These results suggest a novel inhibition mechanism of the hacksaw-like structure, which is different from known inhibitor proteins, through interactions around the characteristic loop regions with the active-site cleft of enzymes. PMID:23091053

  8. Solution structure of IseA, an inhibitor protein of DL-endopeptidases from Bacillus subtilis, reveals a novel fold with a characteristic inhibitory loop.

    PubMed

    Arai, Ryoichi; Fukui, Sadaharu; Kobayashi, Naoya; Sekiguchi, Junichi

    2012-12-28

    In Bacillus subtilis, LytE, LytF, CwlS, and CwlO are vegetative autolysins, DL-endopeptidases in the NlpC/P60 family, and play essential roles in cell growth and separation. IseA (YoeB) is a proteinaceous inhibitor against the DL-endopeptidases, peptidoglycan hydrolases. Overexpression of IseA caused significantly long chained cell morphology, because IseA inhibits the cell separation DL-endopeptidases post-translationally. Here, we report the first three-dimensional structure of IseA, determined by NMR spectroscopy. The structure includes a single domain consisting of three α-helices, one 3(10)-helix, and eight β-strands, which is a novel fold like a "hacksaw." Noteworthy is a dynamic loop between β4 and the 3(10)-helix, which resembles a "blade." The electrostatic potential distribution shows that most of the surface is positively charged, but the region around the loop is negatively charged. In contrast, the LytF active-site cleft is expected to be positively charged. NMR chemical shift perturbation of IseA interacting with LytF indicated that potential interaction sites are located around the loop. Furthermore, the IseA mutants D100K/D102K and G99P/G101P at the loop showed dramatic loss of inhibition activity against LytF, compared with wild-type IseA, indicating that the β4-3(10) loop plays an important role in inhibition. Moreover, we built a complex structure model of IseA-LytF by docking simulation, suggesting that the β4-3(10) loop of IseA gets stuck deep in the cleft of LytF, and the active site is occluded. These results suggest a novel inhibition mechanism of the hacksaw-like structure, which is different from known inhibitor proteins, through interactions around the characteristic loop regions with the active-site cleft of enzymes. PMID:23091053

  9. A novel HIF-1α-integrin-linked kinase regulatory loop that facilitates hypoxia-induced HIF-1α expression and epithelial-mesenchymal transition in cancer cells.

    PubMed

    Chou, Chih-Chien; Chuang, Hsaio-Ching; Salunke, Santosh B; Kulp, Samuel K; Chen, Ching-Shih

    2015-04-10

    Here, we described a novel regulatory feedback loop in which hypoxia induces integrin-linked kinase (ILK) expression through a HIF-1α-dependent mechanism and ILK, in turn, stimulates HIF-1α expression through cell type- and cell context-dependent pathways. HIF-1α increased ILK via transcriptional activation. ILK increased HIF-1α levels by promoting mTOR-mediated translation in PC-3 and MCF-7 cells, and by blocking GSK3β-mediated degradation in LNCaP cells, consistent with the cell line-/cellular context-specific functions of ILK as a Ser473-Akt kinase. We show that ILK can account for the effects of hypoxia on Akt, mTOR, and GSK3β phosphorylation. Also, ILK can de-repress HIF-1α signaling through the YB-1-mediated inhibition of Foxo3a expression. In concert with HIF-1α, these downstream effectors promote epithelial-mesenchymal transition (EMT) through modulation of Snail and Zeb1. Thus, the ILK-HIF-1α regulatory loop could underlie the maintenance of high HIF-1α expression levels and the promotion of EMT under hypoxic conditions. Finally, we show that the small-molecule ILK inhibitor T315 can disrupt this regulatory loop in vivo and suppress xenograft tumor growth, thereby providing proof-of-concept that targeting ILK represents an effective strategy to block HIF-1α expression and aggressive phenotype in cancer cells.

  10. A novel HIF-1α-integrin-linked kinase regulatory loop that facilitates hypoxia-induced HIF-1α expression and epithelial-mesenchymal transition in cancer cells

    PubMed Central

    Chou, Chih-Chien; Chuang, Hsaio-Ching; Salunke, Santosh B.; Kulp, Samuel K.; Chen, Ching-Shih

    2015-01-01

    Here, we described a novel regulatory feedback loop in which hypoxia induces integrin-linked kinase (ILK) expression through a HIF-1α-dependent mechanism and ILK, in turn, stimulates HIF-1α expression through cell type- and cell context-dependent pathways. HIF-1α increased ILK via transcriptional activation. ILK increased HIF-1α levels by promoting mTOR-mediated translation in PC-3 and MCF-7 cells, and by blocking GSK3β-mediated degradation in LNCaP cells, consistent with the cell line-/cellular context-specific functions of ILK as a Ser473-Akt kinase. We show that ILK can account for the effects of hypoxia on Akt, mTOR, and GSK3β phosphorylation. Also, ILK can de-repress HIF-1α signaling through the YB-1-mediated inhibition of Foxo3a expression. In concert with HIF-1α, these downstream effectors promote epithelial-mesenchymal transition (EMT) through modulation of Snail and Zeb1. Thus, the ILK-HIF-1α regulatory loop could underlie the maintenance of high HIF-1α expression levels and the promotion of EMT under hypoxic conditions. Finally, we show that the small-molecule ILK inhibitor T315 can disrupt this regulatory loop in vivo and suppress xenograft tumor growth, thereby providing proof-of-concept that targeting ILK represents an effective strategy to block HIF-1α expression and aggressive phenotype in cancer cells. PMID:25821081

  11. Structural and Inhibitory Effects of Hinge Loop Mutagenesis in Serpin-2 from the Malaria Vector Anopheles gambiae*

    PubMed Central

    Zhang, Xin; Meekins, David A.; An, Chunju; Zolkiewski, Michal; Battaile, Kevin P.; Kanost, Michael R.; Lovell, Scott; Michel, Kristin

    2015-01-01

    Serpin-2 (SRPN2) is a key negative regulator of the melanization response in the malaria vector Anopheles gambiae. SRPN2 irreversibly inhibits clip domain serine proteinase 9 (CLIPB9), which functions in a serine proteinase cascade culminating in the activation of prophenoloxidase and melanization. Silencing of SRPN2 in A. gambiae results in spontaneous melanization and decreased life span and is therefore a promising target for vector control. The previously determined structure of SRPN2 revealed a partial insertion of the hinge region of the reactive center loop (RCL) into β sheet A. This partial hinge insertion participates in heparin-linked activation in other serpins, notably antithrombin III. SRPN2 does not contain a heparin binding site, and any possible mechanistic function of the hinge insertion was previously unknown. To investigate the function of the SRPN2 hinge insertion, we developed three SRPN2 variants in which the hinge regions are either constitutively expelled or inserted and analyzed their structure, thermostability, and inhibitory activity. We determined that constitutive hinge expulsion resulted in a 2.7-fold increase in the rate of CLIPB9Xa inhibition, which is significantly lower than previous observations of allosteric serpin activation. Furthermore, we determined that stable insertion of the hinge region did not appreciably decrease the accessibility of the RCL to CLIPB9. Together, these results indicate that the partial hinge insertion in SRPN2 does not participate in the allosteric activation observed in other serpins and instead represents a molecular trade-off between RCL accessibility and efficient formation of an inhibitory complex with the cognate proteinase. PMID:25525260

  12. Structural integration in hypoxia-inducible factors

    SciTech Connect

    Wu, Dalei; Potluri, Nalini; Lu, Jingping; Kim, Youngchang; Rastinejad, Fraydoon

    2015-08-20

    The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making HIFs attractive anticancer targets. Transcriptionally active HIFs consist of HIF-alpha and ARNT (also called HIF-1 beta) subunits. Here we describe crystal structures for each of mouse HIF-2 alpha-ARNT and HIF-1 alpha-ARNT heterodimers in states that include bound small molecules and their hypoxia response element. A highly integrated quaternary architecture is shared by HIF-2 alpha-ARNT and HIF-1 alpha-ARNT, wherein ARNT spirals around the outside of each HIF-alpha subunit. Five distinct pockets are observed that permit small-molecule binding, including PAS domain encapsulated sites and an interfacial cavity formed through subunit heterodimerization. The DNA-reading head rotates, extends and cooperates with a distal PAS domain to bind hypoxia response elements. HIF-alpha mutations linked to human cancers map to sensitive sites that establish DNA binding and the stability of PAS domains and pockets.

  13. Adaptation of the jejunal mucosa in the experimental blind loop syndrome: changes in paracellular conductance and tight junction structure.

    PubMed

    Schulzke, J D; Fromm, M; Bentzel, C J; Menge, H; Riecken, E O

    1987-01-01

    Self-filling blind loops of rat jejunum exhibit hyperregenerative transformation of the mucosa. We used this experimental model to characterise mechanisms, which may occur under similar conditions in man (stagnant loop syndrome). Epithelial and subepithelial resistance were measured in the Ussing-chamber by voltage divider ratio measurements after positioning a microelectrode between epithelium and subepithelial tissue layers. In the blind loop, epithelial resistance increased from 8 +/- 1 to 23 +/- 1 omega cm2 and subepithelial resistance from 39 +/- 4 to 86 +/- 8 omega cm2 as compared with control jejunum. The increase in the subepithelial resistance was paralleled anatomically by an increase in the thickness of the subepithelial tissue layers from 63 +/- 4 microns to 177 +/- 19 microns. Ultrastructural analysis of the tight junction area by freeze fracture electron microscopy revealed an increase in the total junctional 'depth' in the crypts from 243 +/- 9 nm in control jejunum to 396 +/- 17 nm in the blind loop, while the number of horizontally oriented 'strands' remained unchanged. Villus tight junctions did not differ between blind loop and control. We interpret the alterations in the self-filling blind loop as an adaptive response of the epithelium which reduces backleakage of already absorbed electrolytes across the tight junction into the intestinal lumen. This mechanism is suitable to support the intestine in maintaining body electrolyte and water contents during cellular electrolyte malabsorption.

  14. miR-29b sensitizes multiple myeloma cells to bortezomib-induced apoptosis through the activation of a feedback loop with the transcription factor Sp1

    PubMed Central

    Amodio, N; Di Martino, M T; Foresta, U; Leone, E; Lionetti, M; Leotta, M; Gullà, A M; Pitari, M R; Conforti, F; Rossi, M; Agosti, V; Fulciniti, M; Misso, G; Morabito, F; Ferrarini, M; Neri, A; Caraglia, M; Munshi, N C; Anderson, K C; Tagliaferri, P; Tassone, P

    2012-01-01

    MicroRNAs (miRNAs) with tumor-suppressor potential might have therapeutic applications in multiple myeloma (MM) through the modulation of still undiscovered molecular pathways. Here, we investigated the effects of enforced expression of miR-29b on the apoptotic occurrence in MM and highlighted its role in the context of a new transcriptional loop that is finely tuned by the proteasome inhibitor bortezomib. In details, in vitro growth inhibition and apoptosis of MM cells was induced by either transient expression of synthetic miR-29b or its stable lentivirus-enforced expression. We identified Sp1, a transcription factor endowed with oncogenic activity, as a negative regulator of miR-29b expression in MM cells. Since Sp1 expression and functions are regulated via the 26S proteasome, we investigated the effects of bortezomib on miR-29b-Sp1 loop, showing that miR-29b levels were indeed upregulated by the drug. At the same time, the bortezomib/miR-29b combination produced significant pro-apoptotic effects. We also demonstrated that the PI3K/AKT pathway plays a major role in the regulation of miR-29b-Sp1 loop and induction of apoptosis in MM cells. Finally, MM xenografts constitutively expressing miR-29b showed significant reduction of their tumorigenic potential. Our findings indicate that miR-29b is involved in a regulatory loop amenable of pharmacologic intervention and modulates the anti-MM activity of bortezomib in MM cells. PMID:23190608

  15. miR-29b sensitizes multiple myeloma cells to bortezomib-induced apoptosis through the activation of a feedback loop with the transcription factor Sp1.

    PubMed

    Amodio, N; Di Martino, M T; Foresta, U; Leone, E; Lionetti, M; Leotta, M; Gullà, A M; Pitari, M R; Conforti, F; Rossi, M; Agosti, V; Fulciniti, M; Misso, G; Morabito, F; Ferrarini, M; Neri, A; Caraglia, M; Munshi, N C; Anderson, K C; Tagliaferri, P; Tassone, P

    2012-01-01

    MicroRNAs (miRNAs) with tumor-suppressor potential might have therapeutic applications in multiple myeloma (MM) through the modulation of still undiscovered molecular pathways. Here, we investigated the effects of enforced expression of miR-29b on the apoptotic occurrence in MM and highlighted its role in the context of a new transcriptional loop that is finely tuned by the proteasome inhibitor bortezomib. In details, in vitro growth inhibition and apoptosis of MM cells was induced by either transient expression of synthetic miR-29b or its stable lentivirus-enforced expression. We identified Sp1, a transcription factor endowed with oncogenic activity, as a negative regulator of miR-29b expression in MM cells. Since Sp1 expression and functions are regulated via the 26S proteasome, we investigated the effects of bortezomib on miR-29b-Sp1 loop, showing that miR-29b levels were indeed upregulated by the drug. At the same time, the bortezomib/miR-29b combination produced significant pro-apoptotic effects. We also demonstrated that the PI3K/AKT pathway plays a major role in the regulation of miR-29b-Sp1 loop and induction of apoptosis in MM cells. Finally, MM xenografts constitutively expressing miR-29b showed significant reduction of their tumorigenic potential. Our findings indicate that miR-29b is involved in a regulatory loop amenable of pharmacologic intervention and modulates the anti-MM activity of bortezomib in MM cells. PMID:23190608

  16. MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells

    PubMed Central

    Bleris, Leonidas; Ma, Lan

    2015-01-01

    The p53 tumor suppressor protein plays a critical role in cellular stress and cancer prevention. A number of post-transcriptional regulators, termed microRNAs, are closely connected with the p53-mediated cellular networks. While the molecular interactions among p53 and microRNAs have emerged, a systems-level understanding of the regulatory mechanism and the role of microRNAs-forming feedback loops with the p53 core remains elusive. Here we have identified from literature that there exist three classes of microRNA-mediated feedback loops revolving around p53, all with the nature of positive feedback coincidentally. To explore the relationship between the cellular performance of p53 with the microRNA feedback pathways, we developed a mathematical model of the core p53-MDM2 module coupled with three microRNA-mediated positive feedback loops involving miR-192, miR-34a, and miR-29a. Simulations and bifurcation analysis in relationship to extrinsic noise reproduce the oscillatory behavior of p53 under DNA damage in single cells, and notably show that specific microRNA abrogation can disrupt the wild-type cellular phenotype when the ubiquitous cell-to-cell variability is taken into account. To assess these in silico results we conducted microRNA-perturbation experiments in MCF7 breast cancer cells. Time-lapse microscopy of cell-population behavior in response to DNA double-strand breaks, together with image classification of single-cell phenotypes across a population, confirmed that the cellular p53 oscillations are compromised after miR-192 perturbations, matching well with the model predictions. Our study via modeling in combination with quantitative experiments provides new evidence on the role of microRNA-mediated positive feedback loops in conferring robustness to the system performance of stress-induced response of p53. PMID:26642352

  17. Choking loops on surfaces.

    PubMed

    Feng, Xin; Tong, Yiying

    2013-08-01

    We present a method for computing "choking" loops--a set of surface loops that describe the narrowing of the volumes inside/outside of the surface and extend the notion of surface homology and homotopy loops. The intuition behind their definition is that a choking loop represents the region where an offset of the original surface would get pinched. Our generalized loops naturally include the usual 2g handles/tunnels computed based on the topology of the genus-g surface, but also include loops that identify chokepoints or bottlenecks, i.e., boundaries of small membranes separating the inside or outside volume of the surface into disconnected regions. Our definition is based on persistent homology theory, which gives a measure to topological structures, thus providing resilience to noise and a well-defined way to determine topological feature size. More precisely, the persistence computed here is based on the lower star filtration of the interior or exterior 3D domain with the distance field to the surface being the associated 3D Morse function. PMID:23744260

  18. Suggestive Evidence for the Involvement of the Second Calcium and Surface Loop in Interfacial Binding: Monoclinci and Trigonal Crystal Structures of a Quadruple Mutant of Phospholipase A2

    SciTech Connect

    Sekar,K.; Yogavel, M.; Kanaujia, S.; Sharma, A.; Velmurugan, D.; Poi, M.; Dauter, Z.; Tsai, M.

    2006-01-01

    The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A{sub 2} (PLA{sub 2}) have been solved and refined at 1.9 and 1.1 Angstroms resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.

  19. Diabetes-Induced Oxidative Stress in Endothelial Progenitor Cells May Be Sustained by a Positive Feedback Loop Involving High Mobility Group Box-1.

    PubMed

    Wu, Han; Li, Ran; Wei, Zhong-Hai; Zhang, Xin-Lin; Chen, Jian-Zhou; Dai, Qing; Xie, Jun; Xu, Biao

    2016-01-01

    Oxidative stress is considered to be a critical factor in diabetes-induced endothelial progenitor cell (EPC) dysfunction, although the underlying mechanisms are not fully understood. In this study, we investigated the role of high mobility group box-1 (HMGB-1) in diabetes-induced oxidative stress. HMGB-1 was upregulated in both serum and bone marrow-derived monocytes from diabetic mice compared with control mice. In vitro, advanced glycation end productions (AGEs) induced, expression of HMGB-1 in EPCs and in cell culture supernatants in a dose-dependent manner. However, inhibition of oxidative stress with N-acetylcysteine (NAC) partially inhibited the induction of HMGB-1 induced by AGEs. Furthermore, p66shc expression in EPCs induced by AGEs was abrogated by incubation with glycyrrhizin (Gly), while increased superoxide dismutase (SOD) activity in cell culture supernatants was observed in the Gly treated group. Thus, HMGB-1 may play an important role in diabetes-induced oxidative stress in EPCs via a positive feedback loop involving the AGE/reactive oxygen species/HMGB-1 pathway.

  20. Loop-to-loop coupling.

    SciTech Connect

    Warne, Larry Kevin; Lucero, Larry Martin; Langston, William L.; Salazar, Robert Austin; Coleman, Phillip Dale; Basilio, Lorena I.; Bacon, Larry Donald

    2012-05-01

    This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

  1. Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling

    PubMed Central

    Ferreon, Josephine C.; Hilser, Vincent J.

    2003-01-01

    We report the effects of peptide binding on the 15N relaxation rates and chemical shifts of the C-SH3 of Sem-5. 15N spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and {1H}-15N NOE were obtained from heteronuclear 2D NMR experiments. These parameters were then analyzed using the Lipari-Szabo model free formalism to obtain parameters that describe the internal motions of the protein. High-order parameters (S2 > 0.8) are found in elements of regular secondary structure, whereas some residues in the loop regions show relatively low-order parameters, notably the RT loop. Peptide binding is characterized by a significant decrease in the 15N relaxation in the RT loop. Concomitant with the change in dynamics is a cooperative change in chemical shifts. The agreement between the binding constants calculated from chemical shift differences and that obtained from ITC indicates that the binding of Sem-5 C-SH3 to its putative peptide ligand is coupled to a cooperative conformational change in which a portion of the binding site undergoes a significant reduction in conformational heterogeneity. PMID:12717021

  2. Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop.

    PubMed

    Sahu, P K; Das, B; Sahoo, L; Senapati, S; Nayak, G D

    2016-07-01

    The genetic information obtained from the mitochondrial DNA D-loop region has paramount importance in understanding the evolution of closely related individuals, and designing proper breeding or conservation plans. The present study was conducted using partial D-loop sequences of three local poultry populations from Odisha, India. The partial D-loop sequences were found to be highly polymorphic having 164 polymorphic sites with 89 singletons and 75 parsimony informative sites. Furthermore, 25 insertion and deletion sites were observed. High genetic diversity was observed within three local chicken populations. Highest genetic difference was observed between Gujuri and Kalua population (0.2230) followed by Gujuri and Hansli (0.199) and Kalua with Hansli (0.166). The pairwise mismatch distribution showed that all populations are of constant size over time. Phylogenetic tree analysis indicated that the said three populations were close to the referred population of China, Sri Lanka, Indonesia and Japan than Aseel and Kadaknath (Indian native breeds).

  3. Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation

    PubMed Central

    Bressanelli, Stéphane; Stiasny, Karin; Allison, Steven L; Stura, Enrico A; Duquerroy, Stéphane; Lescar, Julien; Heinz, Franz X; Rey, Félix A

    2004-01-01

    Enveloped viruses enter cells via a membrane fusion reaction driven by conformational changes of specific viral envelope proteins. We report here the structure of the ectodomain of the tick-borne encephalitis virus envelope glycoprotein, E, a prototypical class II fusion protein, in its trimeric low-pH-induced conformation. We show that, in the conformational transition, the three domains of the neutral-pH form are maintained but their relative orientation is altered. Similar to the postfusion class I proteins, the subunits rearrange such that the fusion peptide loops cluster at one end of an elongated molecule and the C-terminal segments, connecting to the viral transmembrane region, run along the sides of the trimer pointing toward the fusion peptide loops. Comparison with the low-pH-induced form of the alphavirus class II fusion protein reveals striking differences at the end of the molecule bearing the fusion peptides, suggesting an important conformational effect of the missing membrane connecting segment. PMID:14963486

  4. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures.

    PubMed

    Mak, Chi H

    2015-11-25

    While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments.

  5. Analysis of the h, H, A → τμ decays induced from SUSY loops within the Mass Insertion Approximation

    NASA Astrophysics Data System (ADS)

    Arganda, E.; Herrero, M. J.; Morales, R.; Szynkman, A.

    2016-03-01

    In this paper we study the lepton favor violating decay channels of the neutral Higgs bosons of the Minimal Supersymmetric Standard Model into a lepton and an anti-lepton of different flavor. We work in the context of the most general flavor mixing scenario in the slepton sector, in contrast to the minimal flavor violation assumption more frequently used. Our analytic computation is a one-loop diagrammatic one, but in contrast to the full one-loop computation which is usually referred to the physical slepton mass basis, we use here instead the Mass Insertion Approximation (MIA) which uses the electroweak interaction slepton basis and treats perturbatively the mass insertions changing slepton flavor. By performing an expansion in powers of the external momenta in the relevant form factors, we will be able to separate explicitly in the analytic results the leading non-decoupling (constant at asymptotically large sparticle masses) and the next to leading decoupling contributions (decreasing with the sparticle masses). Our final aim is to provide a set of simple analytic formulas for the form factors and the associated effective vertices, that we think may be very useful for future phenomenological studies of the lepton flavor violating Higgs boson decays, and for their comparison with data. The accuracy of the numerical results obtained with the MIA are also analyzed and discussed here in comparison with the full one-loop results. Our most optimistic numerical estimates for the three neutral Higgs boson decays channels into τ and μ leptons, searching for their maximum rates that are allowed by present constraints from τ → μγ data and beyond Standard Model Higgs boson searches at the LHC, are also included.

  6. Identification of a negative feedback loop between cyclic di-GMP-induced levels of IFI16 and p202 cytosolic DNA sensors and STING.

    PubMed

    Panchanathan, Ravichandran; Liu, Hongzhu; Xin, Duan; Choubey, Divaker

    2014-10-01

    A host type I IFN response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP (c-di-GMP) by STING (stimulator of IFN genes). Because the STING, an adaptor protein, links the cytosolic detection of DNA by the cytosolic DNA sensors such as the IFN-inducible human IFI16 and murine p202 proteins to the TBK1/IRF3 axis, we investigated whether c-di-GMP-induced signaling could regulate expression of IFI16 and p202 proteins. Here, we report that activation of c-di-GMP-induced signaling in human and murine cells increased steady-state levels of IFI16 and p202 proteins. The increase was c-di-GMP concentration- and time-dependent. Unexpectedly, treatment of cells with type I IFN decreased levels of the adaptor protein STING. Therefore, we investigated whether the IFI16 or p202 protein could regulate the expression of STING and activation of the TBK1/IRF3 axis. We found that constitutive knockdown of IFI16 or p202 expression in cells increased steady-state levels of STING. Additionally, the knockdown of IFI16 resulted in activation of the TBK1/IRF3 axis. Accordingly, increased levels of the IFI16 or p202 protein in cells decreased STING levels. Together, our observations identify a novel negative feedback loop between c-di-GMP-induced levels of IFI16 and p202 cytosolic DNA sensors and the adaptor protein STING.

  7. Evolution in a Braided Loop Ensemble

    NASA Video Gallery

    This braided loop has several loops near the 'base' that appear to be unwinding with significant apparent outflow. This is evidence of untwisting, and the braided structure also seeming to unwind w...

  8. Commitment in Structurally Enabled and Induced Exchange Relations

    ERIC Educational Resources Information Center

    Lawler, Edward J.; Thye, Shane R.; Yoon, Jeongkoo

    2006-01-01

    Network structures both enable and constrain the development of social relations. This research investigates these features by comparing the development of commitments in structurally enabled and structurally induced exchange relations. We integrate ideas from the theory of relational cohesion and the choice process theory of commitment. In an…

  9. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex.

    PubMed

    Angulo, Jenniffer; Ulryck, Nathalie; Deforges, Jules; Chamond, Nathalie; Lopez-Lastra, Marcelo; Masquida, Benoît; Sargueil, Bruno

    2016-02-18

    As obligatory intracellular parasites, viruses rely on cellular machines to complete their life cycle, and most importantly they recruit the host ribosomes to translate their mRNA. The Hepatitis C viral mRNA initiates translation by directly binding the 40S ribosomal subunit in such a way that the initiation codon is correctly positioned in the P site of the ribosome. Such a property is likely to be central for many viruses, therefore the description of host-pathogen interaction at the molecular level is instrumental to provide new therapeutic targets. In this study, we monitored the 40S ribosomal subunit and the viral RNA structural rearrangement induced upon the formation of the binary complex. We further took advantage of an IRES viral mutant mRNA deficient for translation to identify the interactions necessary to promote translation. Using a combination of structure probing in solution and molecular modeling we establish a whole atom model which appears to be very similar to the one obtained recently by cryoEM. Our model brings new information on the complex, and most importantly reveals some structural rearrangement within the ribosome. This study suggests that the formation of a 'kissing complex' between the viral RNA and the 18S ribosomal RNA locks the 40S ribosomal subunit in a conformation proficient for translation. PMID:26626152

  10. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex

    PubMed Central

    Angulo, Jenniffer; Ulryck, Nathalie; Deforges, Jules; Chamond, Nathalie; Lopez-Lastra, Marcelo; Masquida, Benoît; Sargueil, Bruno

    2016-01-01

    As obligatory intracellular parasites, viruses rely on cellular machines to complete their life cycle, and most importantly they recruit the host ribosomes to translate their mRNA. The Hepatitis C viral mRNA initiates translation by directly binding the 40S ribosomal subunit in such a way that the initiation codon is correctly positioned in the P site of the ribosome. Such a property is likely to be central for many viruses, therefore the description of host-pathogen interaction at the molecular level is instrumental to provide new therapeutic targets. In this study, we monitored the 40S ribosomal subunit and the viral RNA structural rearrangement induced upon the formation of the binary complex. We further took advantage of an IRES viral mutant mRNA deficient for translation to identify the interactions necessary to promote translation. Using a combination of structure probing in solution and molecular modeling we establish a whole atom model which appears to be very similar to the one obtained recently by cryoEM. Our model brings new information on the complex, and most importantly reveals some structural rearrangement within the ribosome. This study suggests that the formation of a ‘kissing complex’ between the viral RNA and the 18S ribosomal RNA locks the 40S ribosomal subunit in a conformation proficient for translation. PMID:26626152

  11. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex.

    PubMed

    Angulo, Jenniffer; Ulryck, Nathalie; Deforges, Jules; Chamond, Nathalie; Lopez-Lastra, Marcelo; Masquida, Benoît; Sargueil, Bruno

    2016-02-18

    As obligatory intracellular parasites, viruses rely on cellular machines to complete their life cycle, and most importantly they recruit the host ribosomes to translate their mRNA. The Hepatitis C viral mRNA initiates translation by directly binding the 40S ribosomal subunit in such a way that the initiation codon is correctly positioned in the P site of the ribosome. Such a property is likely to be central for many viruses, therefore the description of host-pathogen interaction at the molecular level is instrumental to provide new therapeutic targets. In this study, we monitored the 40S ribosomal subunit and the viral RNA structural rearrangement induced upon the formation of the binary complex. We further took advantage of an IRES viral mutant mRNA deficient for translation to identify the interactions necessary to promote translation. Using a combination of structure probing in solution and molecular modeling we establish a whole atom model which appears to be very similar to the one obtained recently by cryoEM. Our model brings new information on the complex, and most importantly reveals some structural rearrangement within the ribosome. This study suggests that the formation of a 'kissing complex' between the viral RNA and the 18S ribosomal RNA locks the 40S ribosomal subunit in a conformation proficient for translation.

  12. Determination of the structure and heating mechanisms of coronal loops from soft X-ray observations with the solar probe. [grazing incidence telescope

    NASA Technical Reports Server (NTRS)

    Davis, J. M.; Krieger, A. S.

    1978-01-01

    High resolution soft X-ray imaging from the solar probe is justified in terms of the expected scientific returns which include the determination of the temperature and density structure of a coronal loop. The advantages of the grazing incidence telescope over the multiple pinhole camera are discussed. An instrument package is described which includes a grazing incidence mirror, a thermal prefilter, a three position filter wheel and a focal plane detector baselined as an 800 by 800 back-illuminated charge coupled device. The structural assembly together with the data processing equipment would draw heavily on the designs being developed for the Solar Polar Mission.

  13. A novel hypoxia-induced miR-147a regulates cell proliferation through a positive feedback loop of stabilizing HIF-1α

    PubMed Central

    Wang, Fan; Zhang, Haoxiang; Xu, Naihan; Huang, Nunu; Tian, Caiming; Ye, Anlin; Hu, Guangnan; He, Jie; Zhang, Yaou

    2016-01-01

    ABSTRACT Hypoxia is a general event in solid tumor growth. Therefore, induced cellular responses by hypoxia are important for tumorigenesis and tumor growth. MicroRNAs (miRNAs) have recently emerged as important regulators of hypoxia induced cellular responses. Here we report that miR-147a is a novel and crucial hypoxia induced miRNA. HIF-1α up-regulates the expression of miR-147a, and miR-147a in turn stabilizes and accumulates HIF-1α protein via directly targeting HIF-3α, a dominant negative regulator of HIF-1α. Subsequent studies in xenograft mouse model reveal that miR-147a is capable of inhibiting tumor growth. Collectively, these data demonstrate a positive feedback loop between HIF-1α, miR-147a and HIF-3α, which provide a new insight into the mechanism of miR-147a induced cell proliferation arrest under hypoxia. PMID:27260617

  14. Open and closed cortico-subcortical loops: A neuro-computational account of access to consciousness in the distractor-induced blindness paradigm.

    PubMed

    Ebner, Christian; Schroll, Henning; Winther, Gesche; Niedeggen, Michael; Hamker, Fred H

    2015-09-01

    How the brain decides which information to process 'consciously' has been debated over for decades without a simple explanation at hand. While most experiments manipulate the perceptual energy of presented stimuli, the distractor-induced blindness task is a prototypical paradigm to investigate gating of information into consciousness without or with only minor visual manipulation. In this paradigm, subjects are asked to report intervals of coherent dot motion in a rapid serial visual presentation (RSVP) stream, whenever these are preceded by a particular color stimulus in a different RSVP stream. If distractors (i.e., intervals of coherent dot motion prior to the color stimulus) are shown, subjects' abilities to perceive and report intervals of target dot motion decrease, particularly with short delays between intervals of target color and target motion. We propose a biologically plausible neuro-computational model of how the brain controls access to consciousness to explain how distractor-induced blindness originates from information processing in the cortex and basal ganglia. The model suggests that conscious perception requires reverberation of activity in cortico-subcortical loops and that basal-ganglia pathways can either allow or inhibit this reverberation. In the distractor-induced blindness paradigm, inadequate distractor-induced response tendencies are suppressed by the inhibitory 'hyperdirect' pathway of the basal ganglia. If a target follows such a distractor closely, temporal aftereffects of distractor suppression prevent target identification. The model reproduces experimental data on how delays between target color and target motion affect the probability of target detection.

  15. A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326

    PubMed Central

    Luthra, Amit; Anand, Arvind; Hawley, Kelly L.; LeDoyt, Morgan; La Vake, Carson J.; Caimano, Melissa J.; Cruz, Adriana R.; Salazar, Juan C.

    2015-01-01

    ABSTRACT We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu593 → Gln593) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a “structure-to-pathogenesis” approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. IMPORTANCE Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog

  16. Structural and Catalytic Effects of Proline Substitution and Surface Loop Deletion in the Extended Active Site of Human Carbonic Anhydrase II

    PubMed Central

    Boone, Christopher D.; Rasi, Valerio; Tu, Chingkuang; McKenna, Robert

    2015-01-01

    The bioengineering of a thermophilic enzyme starting from a mesophilic scaffold has proven to be a significant challenge as several stabilizing elements have been proposed to be the foundation of thermal stability including disulfide bridges, surface loop reduction, ionic pair networks, proline substitutions, and aromatic clusters. This study emphasizes the impact of increasing the rigidity of human carbonic anhydrase II (HCA II) via incorporation of proline residues at positions 170 and 234, which are located in surface loops that are able to accommodate restrictive main-chain conformations without rearrangement of the surrounding peptide backbone. Additionally, the effect of compactness of HCA II was examined by way of deletion of a surface loop (residues 230 through 240), which had been previously identified as a possible source of thermal stability for the hyperthermophilic CA isolated from the bacterium Sulfurihydrogenibium yellowstonense YO3AOP1. Differential scanning calorimetry analysis of these HCA II variants revealed that these structural modifications had a minimum effect on the thermal stability of the enzyme while kinetic studies showed unexpected effects on the catalytic efficiency and proton transfer rates. X-ray crystallographic analysis of these HCA II variants showed the electrostatic potential and configuration of the highly acidic loop (residues 230 and 240) plays an important role in its high catalytic activity. Based on these observations and the literature, a picture is emerging of the various components within the general structural architecture of HCA II that are key to stability. These elements could provide the blueprints for the rational thermal stability engineering of other enzymes. PMID:25683338

  17. Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line

    PubMed Central

    Siciliano, Velia; Fracassi, Chiara; Garzilli, Immacolata; Moretti, Maria Nicoletta; di Bernardo, Diego

    2011-01-01

    Understanding the relationship between topology and dynamics of transcriptional regulatory networks in mammalian cells is essential to elucidate the biology of complex regulatory and signaling pathways. Here, we characterised, via a synthetic biology approach, a transcriptional positive feedback loop (PFL) by generating a clonal population of mammalian cells (CHO) carrying a stable integration of the construct. The PFL network consists of the Tetracycline-controlled transactivator (tTA), whose expression is regulated by a tTA responsive promoter (CMV-TET), thus giving rise to a positive feedback. The same CMV-TET promoter drives also the expression of a destabilised yellow fluorescent protein (d2EYFP), thus the dynamic behaviour can be followed by time-lapse microscopy. The PFL network was compared to an engineered version of the network lacking the positive feedback loop (NOPFL), by expressing the tTA mRNA from a constitutive promoter. Doxycycline was used to repress tTA activation (switch off), and the resulting changes in fluorescence intensity for both the PFL and NOPFL networks were followed for up to 43 h. We observed a striking difference in the dynamics of the PFL and NOPFL networks. Using non-linear dynamical models, able to recapitulate experimental observations, we demonstrated a link between network topology and network dynamics. Namely, transcriptional positive autoregulation can significantly slow down the “switch off” times, as comparared to the nonautoregulatated system. Doxycycline concentration can modulate the response times of the PFL, whereas the NOPFL always switches off with the same dynamics. Moreover, the PFL can exhibit bistability for a range of Doxycycline concentrations. Since the PFL motif is often found in naturally occurring transcriptional and signaling pathways, we believe our work can be instrumental to characterise their behaviour. PMID:21765813

  18. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states

    PubMed Central

    Baranowski, Maciej; Ołldziej, Stanisław; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary

    2013-01-01

    The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of large proteins effectively. It performs well in ab initio predictions of protein structure, as demonstrated in the last Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). However, the resolution of the simulated structure is too coarse, especially in loop regions, which results from insufficient specificity of the model of local interactions. To improve the representation of local interactions, in this work we introduced new side-chain-backbone correlation potentials, derived from a statistical analysis of loop regions of 4585 proteins. To obtain sufficient statistics, we reduced the set of amino-acid-residue types to five groups, derived in our earlier work on structurally optimized reduced alphabets, based on a statistical analysis of the properties of amino-acid structures. The new correlation potentials are expressed as one-dimensional Fourier series in the virtual-bond-dihedral angles involving side-chain centroids. The weight of these new terms was determined by a trial-and-error method, in which Multiplexed Replica Exchange Molecular Dynamics (MREMD) simulations were run on selected test proteins. The best average root-mean-square deviations (RMSDs) of the calculated structures from the experimental structures below the folding-transition temperatures were obtained with the weight of the new side-chain-backbone correlation potentials equal to 0.57. The resulting conformational ensembles were analyzed in detail by using the Weighted Histogram Analysis Method (WHAM) and Ward's minimum-variance clustering. This analysis showed that the RMSDs from the experimental structures dropped by 0.5 Å on average, compared to simulations without the new terms, and the deviation of individual residues in the loop region of the computed

  19. Detection of cystic structures using pulsed ultrasonically induced resonant cavitation

    NASA Technical Reports Server (NTRS)

    Bar-Cohen, Yoseph (Inventor); Kovach, John S. (Inventor)

    2002-01-01

    Apparatus and method for early detection of cystic structures indicative of ovarian and breast cancers uses ultrasonic wave energy at a unique resonance frequency for inducing cavitation in cystic fluid characteristic of cystic structures in the ovaries associated with ovarian cancer, and in cystic structures in the breast associated with breast cancer. Induced cavitation bubbles in the cystic fluid implode, creating implosion waves which are detected by ultrasonic receiving transducers attached to the abdomen of the patient. Triangulation of the ultrasonic receiving transducers enables the received signals to be processed and analyzed to identify the location and structure of the cyst.

  20. All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.

    PubMed

    Burakova, Ludmila P; Natashin, Pavel V; Malikova, Natalia P; Niu, Fengfeng; Pu, Mengchen; Vysotski, Eugene S; Liu, Zhi-Jie

    2016-01-01

    Light-sensitive photoprotein berovin accounts for a bright bioluminescence of ctenophore Beroe abyssicola. Berovin is functionally identical to the well-studied Ca(2+)-regulated photoproteins of jellyfish, however in contrast to those it is extremely sensitive to the visible light. Berovin contains three EF-hand Ca(2+)-binding sites and consequently belongs to a large family of the EF-hand Ca(2+)-binding proteins. Here we report the spatial structure of apo-berovin with bound Mg(2+) determined at 1.75Å. The magnesium ion is found in each functional EF-hand loop of a photoprotein and coordinated by oxygen atoms donated by the side-chain groups of aspartate, carbonyl groups of the peptide backbone, or hydroxyl group of serine with characteristic oxygen-Mg(2+) distances. As oxygen supplied by the side-chain of the twelfth residue of all Ca(2+)-binding loops participates in the magnesium ion coordination, it was suggested that Ca(2+)-binding loops of berovin belong to the mixed Ca(2+)/Mg(2+) rather than Ca(2+)-specific type. In addition, we report an effect of physiological concentration of Mg(2+) on bioluminescence of berovin (sensitivity to Ca(2+), rapid-mixed kinetics, light-sensitivity, thermostability, and apo-berovin conversion into active protein). The different impact of physiological concentration of Mg(2+) on berovin bioluminescence as compared to hydromedusan photoproteins was attributed to different affinities of the Ca(2+)-binding sites of these photoproteins to Mg(2+). PMID:26690016

  1. All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.

    PubMed

    Burakova, Ludmila P; Natashin, Pavel V; Malikova, Natalia P; Niu, Fengfeng; Pu, Mengchen; Vysotski, Eugene S; Liu, Zhi-Jie

    2016-01-01

    Light-sensitive photoprotein berovin accounts for a bright bioluminescence of ctenophore Beroe abyssicola. Berovin is functionally identical to the well-studied Ca(2+)-regulated photoproteins of jellyfish, however in contrast to those it is extremely sensitive to the visible light. Berovin contains three EF-hand Ca(2+)-binding sites and consequently belongs to a large family of the EF-hand Ca(2+)-binding proteins. Here we report the spatial structure of apo-berovin with bound Mg(2+) determined at 1.75Å. The magnesium ion is found in each functional EF-hand loop of a photoprotein and coordinated by oxygen atoms donated by the side-chain groups of aspartate, carbonyl groups of the peptide backbone, or hydroxyl group of serine with characteristic oxygen-Mg(2+) distances. As oxygen supplied by the side-chain of the twelfth residue of all Ca(2+)-binding loops participates in the magnesium ion coordination, it was suggested that Ca(2+)-binding loops of berovin belong to the mixed Ca(2+)/Mg(2+) rather than Ca(2+)-specific type. In addition, we report an effect of physiological concentration of Mg(2+) on bioluminescence of berovin (sensitivity to Ca(2+), rapid-mixed kinetics, light-sensitivity, thermostability, and apo-berovin conversion into active protein). The different impact of physiological concentration of Mg(2+) on berovin bioluminescence as compared to hydromedusan photoproteins was attributed to different affinities of the Ca(2+)-binding sites of these photoproteins to Mg(2+).

  2. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism

    PubMed Central

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-01-01

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOTTM). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen. PMID:26563565

  3. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

    PubMed

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-11-13

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.

  4. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

    PubMed

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-01-01

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen. PMID:26563565

  5. Stem-loop SL4 of the HIV-1 psi RNA packaging signal exhibits weak affinity for the nucleocapsid protein. structural studies and implications for genome recognition.

    PubMed

    Amarasinghe, G K; Zhou, J; Miskimon, M; Chancellor, K J; McDonald, J A; Matthews, A G; Miller, R R; Rouse, M D; Summers, M F

    2001-12-14

    Encapsidation of the genome of the human immunodeficiency virus type-1 (HIV-1) during retrovirus assembly is mediated by interactions between the nucleocapsid (NC) domains of assembling Gag polyproteins and a approximately 110 nucleotide segment of the genome known as the Psi-site. The HIV-1 Psi-site contains four stem-loops (SL1 through SL4), all of which are important for genome packaging. Recent isothermal titration calorimetry (ITC) studies have demonstrated that SL2 and SL3 are capable of binding NC with high affinity (K(d) approximately 140 nM), consistent with proposals for protein-interactive functions during packaging. To determine if SL4 may have a similar function, NC-interactive studies were conducted by NMR and gel-shift methods. In contrast to previous reports, we find that SL4 binds weakly to NC (K(d)=(+/-14 microM), suggesting an alternative function. NMR studies indicate that the GAGA tetraloop of SL4 adopts a classical GNRA-type fold (R=purine, N=G, C, A or U), a motif that stabilizes RNA tertiary structures in other systems. In combination with previously reported gel mobility studies of Psi-site deletion mutants, these findings suggest that SL4 functions in genome recognition not by binding to Gag, but by stabilizing the structure of the Psi-site. Differences in the affinities of NC for SL2, SL3 and SL4 stem-loops can now be rationalized in terms of the different structural properties of stem loops that contain GGNG (SL2 and SL3) and GNRA (SL4) sequences.

  6. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

    SciTech Connect

    Lewis, M.; Chang, G.; Horton, N.C.

    1996-03-01

    The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor a product of the lacl gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-B-D-1thiogalactoside (IPTG) and the lac repressor complexed with a 21 base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and the repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quarternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites in the genomic DNA. 76 refs., 11 figs., 1 tab.

  7. Structural fluctuation of proteins induced by thermodynamic perturbation

    SciTech Connect

    Hirata, Fumio; Akasaka, Kazuyuki

    2015-01-28

    A theory to describe structural fluctuations of protein induced by thermodynamic perturbations, pressure, temperature, and denaturant, is proposed. The theory is formulated based on the three methods in the statistical mechanics: the generalized Langevin theory, the linear response theory, and the three dimensional interaction site model (3D-RISM) theory. The theory clarifies how the change in thermodynamic conditions, or a macroscopic perturbation, induces the conformational fluctuation, which is a microscopic property. The theoretical results are applied, on the conceptual basis, to explain the experimental finding by Akasaka et al., concerning the NMR experiment which states that the conformational change induced by pressure corresponds to structural fluctuations occurring in the ambient condition. A method to evaluate the structural fluctuation induced by pressure is also suggested by means of the 3D-RISM and the site-site Kirkwood-Buff theories.

  8. An inducible autoregulatory loop between HIPK2 and Siah2 at the apex of the hypoxic response.

    PubMed

    Calzado, Marco A; de la Vega, Laureano; Möller, Andreas; Bowtell, David D L; Schmitz, M Lienhard

    2009-01-01

    Oxygen deprivation (hypoxia) results in reprogrammed gene expression patterns that induce multifaceted cellular responses. Here we identify a regulated interaction between the serine/threonine kinase HIPK2 and the ubiquitin E3 ligase Siah2 as a mechanism controlling the hypoxic response. Under normoxic conditions, several mechanisms ensure HIPK2 stability: only a fraction of HIPK2 is found in association with Siah2, whereas HIPK2-mediated phosphorylation of this E3 ligase at positions 26, 28 and 68 weakens mutual binding and destabilizes its phosphorylated interaction partner. Hypoxic conditions allow a markedly increased HIPK2/Siah2 interaction and result in efficient polyubiquitylation and proteasomal degradation of the kinase. Accordingly, hypoxia-induced HIPK2 elimination is markedly reduced in Siah2-deficient cells. As HIPK2 has an important role as a negative regulator of gene expression, its elimination from promoter-associated repressor complexes allows the induction of a substantial fraction of hypoxia-induced genes.

  9. Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies.

    PubMed Central

    Germann, M W; Kalisch, B W; Lundberg, P; Vogel, H J; van de Sande, J H

    1990-01-01

    We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzyme and also showed only weak binding to EcoRI in the absence of the cofactor Mg2+. In contrast, hairpins with larger loops are hydrolyzed by the enzyme at the scission site next to the loop although the substrate with a A4 loop is significantly more resistant than the oligonucleotide containing a T4 loop. The hairpin structures with 3 loop residues were found to be thermally most stable while larger hairpin loops resulted in structures with lower melting temperatures. The T-loop hairpins are thermally more stable than the hairpins containing the same number of A residues in the loop. As judged from proton NMR spectroscopy and the thermodynamic data, the base pair closest to the hairpin loop did form in all cases studied. The hairpin loops did, however, affect the conformation of the stem structure of the hairpins. From 31P and 1H NMR spectroscopy we conclude that the perturbation of the stem structure is stronger for smaller hairpin loops and that the extent of the perturbation is limited to 2-3 base pairs for hairpins with T3 or A4 loops. Our results demonstrate that hairpin loops modulate the conformation of the stem residues close to the loop and that this in turn reduces the substrate activity for DNA sequence specific proteins. Images PMID:2326190

  10. Higher dimensional loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2016-07-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n+1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n+1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n+1 dimensional model and the 3+1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology.

  11. Loop-bed combustion apparatus

    DOEpatents

    Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

    1984-01-01

    The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

  12. Pressure-induced structural changes of HBr

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Sprik, Michiel; Terakura, Kiyoyuki; Parrinello, Michele

    1999-04-01

    First-principles molecular dynamics simulation of solid HBr under pressure has been performed using the Car-Parrinello method. A detailed study of the pressure response of the vibrational and proton-transfer dynamics showed that the phase I can be described as a rotator phase with fluctuating hydrogen bonds up to ∼10 GPa. We reproduced the shoulder-like structure seen in the infrared spectra of the H-Br stretching mode in the disordered phase.

  13. Structural changes of linear DNA molecules induced by cisplatin

    SciTech Connect

    Liu, Zhiguo; Liu, Ruisi; Zhou, Zhen; Zu, Yuangang; Xu, Fengjie

    2015-02-20

    Interaction between long DNA molecules and activated cisplatin is believed to be crucial to anticancer activity. However, the exact structural changes of long DNA molecules induced by cisplatin are still not very clear. In this study, structural changes of long linear double-stranded DNA (dsDNA) and short single-stranded DNA (ssDNA) induced by activated cisplatin have been investigated by atomic force microscopy (AFM). The results indicated that long DNA molecules gradually formed network structures, beads-on-string structures and their large aggregates. Electrostatic and coordination interactions were considered as the main driving forces producing these novel structures. An interesting finding in this study is the beads-on-string structures. Moreover, it is worth noting that the beads-on-string structures were linked into the networks, which can be ascribed to the strong DNA–DNA interactions. This study expands our knowledge of the interactions between DNA molecules and cisplatin. - Highlights: • We investigate structural changes of dsDNA and ssDNA induced by cisplatin. • AFM results indicated long dsDNA formed network, beads-on-string and aggregates. • ssDNA can form very similar structures as those of long linear dsDNA. • A possible formation process of theses novel structure is proposed.

  14. Ultrahigh and High Resolution Structures and Mutational Analysis of Monomeric Streptococcus pyogenes SpeB Reveal a Functional Role for the Glycine-rich C-terminal Loop

    SciTech Connect

    González-Páez, Gonzalo E.; Wolan, Dennis W.

    2012-09-05

    Cysteine protease SpeB is secreted from Streptococcus pyogenes and has been studied as a potential virulence factor since its identification almost 70 years ago. Here, we report the crystal structures of apo mature SpeB to 1.06 {angstrom} resolution as well as complexes with the general cysteine protease inhibitor trans-epoxysuccinyl-L-leucylamido(4-guanidino)butane and a novel substrate mimetic peptide inhibitor. These structures uncover conformational changes associated with maturation of SpeB from the inactive zymogen to its active form and identify the residues required for substrate binding. With the use of a newly developed fluorogenic tripeptide substrate to measure SpeB activity, we determined IC{sub 50} values for trans-epoxysuccinyl-L-leucylamido(4-guanidino)butane and our new peptide inhibitor and the effects of mutations within the C-terminal active site loop. The structures and mutational analysis suggest that the conformational movements of the glycine-rich C-terminal loop are important for the recognition and recruitment of biological substrates and release of hydrolyzed products.

  15. Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses

    PubMed Central

    Firth, Andrew E; Wang, Qing S; Jan, Eric; Atkins, John F

    2009-01-01

    The family Dicistroviridae (order Picornavirales) includes species that infect insects and other arthropods. These viruses have a linear positive-sense ssRNA genome of ~8-10 kb, which contains two long ORFs. The 5' ORF encodes the nonstructural polyprotein while the 3' ORF encodes the structural polyprotein. The dicistroviruses are noteworthy for the intergenic Internal Ribosome Entry Site (IGR-IRES) that mediates efficient translation initation on the 3' ORF without the requirement for initiator Met-tRNA. Acute bee paralysis virus, Israel acute paralysis virus of bees and Kashmir bee virus form a distinct subgroup within the Dicistroviridae family. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF in these viruses. The ORF overlaps the 5' end of the structural polyprotein coding sequence in the +1 reading frame. We also identify a potential 14-18 bp RNA stem-loop structure 5'-adjacent to the IGR-IRES. We discuss potential translation initiation mechanisms for the novel ORF in the context of the IGR-IRES and 5'-adjacent stem-loop. PMID:19895695

  16. Site-directed mutagenesis of the glycine-rich loop of death associated protein kinase (DAPK) identifies it as a key structure for catalytic activity.

    PubMed

    McNamara, Laurie K; Brunzelle, Joseph S; Schavocky, James P; Watterson, D Martin; Grum-Tokars, Valerie

    2011-05-01

    Death associated protein kinase (DAPK) is a calmodulin (CaM)-regulated protein kinase that is a therapeutic target for central nervous system (CNS) disorders. We report here the results of studies that test the hypothesis of McNamara et al. (2009) that conformational selection in DAPK's glycine-rich region is key for catalytic activity. The hypothesis was tested by site-directed mutagenesis of glutamine-23 (Q23) in the middle of this loop. The glycine-rich loop exhibits localized differences in structure among DAPK conformations that correlate with different stages of the catalytic cycle. Changing the Q23 to a Valine (V23), found at the corresponding position in another CaM regulated protein kinase, results in a reduced catalytic efficiency. High resolution X-ray crystal structures of various conformations of the Q23V mutant DAPK and their superimposition with the corresponding conformations from wild type catalytic domain reveal localized changes in the glycine-rich region. The effect of the mutation on DAPK catalytic activity and the finding of only localized changes in the DAPK structure provide experimental evidence implicating conformational selection in this domain with activity. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.

  17. Mechanism of acoustically induced diffusional structuring of surface adatoms

    SciTech Connect

    Wu, Chengping; Zhigilei, Leonid V.; Zaitsev, Vladimir Yu.

    2013-11-25

    Physical mechanisms of time-averaged structuring of adatoms induced by a standing surface acoustic wave (SAW) on a solid substrate are studied. Despite some similarity with conventional mechanisms based on averaging of fast oscillation-type motion or radiation-pressure effects, we demonstrate that, for diffusional (i.e., strongly damped) adatom motion, the origin of time-averaged structuring is essentially different. The proposed analytical model and kinetic Monte–Carlo (kMC) simulations reveal several distinct structuring regimes and directly relate them to the transient modification of diffusion barriers and adiabatic temperature variations induced by SAW strains.

  18. A new moon-induced structure

    NASA Astrophysics Data System (ADS)

    Albers, Nicole

    2014-11-01

    Cassini UVIS stellar occultations show prominent gaps within Saturn's ring located only a few km from the Encke and Keeler gap edges. These transparent regions feature sharp edges and measure a few km in radial width. Already the Voyager 2 PPS experiment registered such a gap near the inner Encke gap edge.All gaps identified so far have been found exclusively downstream of the embedded moons Pan and Daphnis, respectively. Interestingly, none has been observed at the inner Keeler gap edge, where temporal and spatial variability of the edge are still poorly understood and most likely driven by the Prometheus 32:31 ILR located nearby. There is evidence for a weak trend between radial width and relative azimuthal distance to the moon. Trends for features found near the inner and outer Encke gap edge are consistent with each other. Two occultations, one tracking and one double star occultation, allow to investigate spatial and temporal morphology of these gaps. Our preliminary results suggest that these structures are individual gaps with an aspect ratio of about 1:5 and may thus be about 10km long.Embedded moons are known to create observable structures - gaps and kinematic wakes - in the surrounding ring. While Pan and Daphnis are massive enough to open a circumferential gap, smaller objects create the propeller features. These new results, however, reveal the existence of a previously unknown and unpredicted moon-associated structure. Its existence offers another avenue in searching for embedded objects, although our preliminary search did not produce examples apart from those reported here for Pan and Daphnis.We acknowledge Tracy Becker for providing an initial list of positive detections. This work is supported by the Cassini project.

  19. Supersymmetric structure of the induced W gravities

    NASA Astrophysics Data System (ADS)

    Ader, Jean-Pierre; Biet, Franck; Noirot, Yves

    1999-03-01

    We derive the supersymmetric structure present in W-gravities which has been already observed in various contexts as Yang-Mills theory, topological field theories, bosonic string and chiral 0264-9381/16/3/029/img2-gravity. This derivation which is made in the geometrical framework of Zucchini, necessitates the introduction of an appropriate new basis of variables which replace the canonical fields and their derivatives. This construction is used, in the 0264-9381/16/3/029/img3-case, to deduce from the Chern-Simons action the Wess-Zumino-Polyakov action.

  20. Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops

    SciTech Connect

    Kwon, Young Do; Finzi, Andrés; Wu, Xueling; Dogo-Isonagie, Cajetan; Lee, Lawrence K.; Moore, Lucas R.; Schmidt, Stephen D.; Stuckey, Jonathan; Yang, Yongping; Zhou, Tongqing; Zhu, Jiang; Vicic, David A.; Debnath, Asim K.; Shapiro, Lawrence; Bewley, Carole A.; Mascola, John R.; Sodroski, Joseph G.; Kwong, Peter D.

    2013-03-04

    The HIV-1 envelope (Env) spike (gp120{sub 3}/gp41{sub 3}) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation and primes Env for entry. The CD4-bound state, however, is prone to spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1 maintain CD4-binding capacity and regulate transitions to the CD4-bound state? To define this mechanistically, we determined crystal structures of unliganded core gp120 from HIV-1 clades B, C, and E. Notably, all of these unliganded HIV-1 structures resembled the CD4-bound state. Conformational fixation with ligand selection and thermodynamic analysis of full-length and core gp120 interactions revealed that the tendency of HIV-1 gp120 to adopt the CD4-bound conformation was restrained by the V1/V2- and V3-variable loops. In parallel, we determined the structure of core gp120 in complex with the small molecule, NBD-556, which specifically recognizes the CD4-bound conformation of gp120. Neutralization by NBD-556 indicated that Env spikes on primary isolates rarely assume the CD4-bound conformation spontaneously, although they could do so when quaternary restraints were loosened. Together, the results suggest that the CD4-bound conformation represents a 'ground state' for the gp120 core, with variable loop and quaternary interactions restraining unliganded gp120 from 'snapping' into this conformation. A mechanism of control involving deformations in unliganded structure from a functionally critical state (e.g., the CD4-bound state) provides advantages in terms of HIV-1 Env structural diversity and resistance to antibodies and inhibitors, while maintaining elements essential for entry.

  1. A Mutation within the Extended X Loop Abolished Substrate-induced ATPase Activity of the Human Liver ATP-binding Cassette (ABC) Transporter MDR3*

    PubMed Central

    Kluth, Marianne; Stindt, Jan; Dröge, Carola; Linnemann, Doris; Kubitz, Ralf; Schmitt, Lutz

    2015-01-01

    The human multidrug resistance protein 3 (MDR3/ABCB4) belongs to the ubiquitous family of ATP-binding cassette (ABC) transporters and is located in the canalicular membrane of hepatocytes. There it flops the phospholipids of the phosphatidylcholine (PC) family from the inner to the outer leaflet. Here, we report the characterization of wild type MDR3 and the Q1174E mutant, which was identified previously in a patient with progressive familial intrahepatic cholestasis type 3 (PFIC-3). We expressed different variants of MDR3 in the yeast Pichia pastoris, purified the proteins via tandem affinity chromatography, and determined MDR3-specific ATPase activity in the presence or absence of phospholipids. The ATPase activity of wild type MDR3 was stimulated 2-fold by liver PC or 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine lipids. Furthermore, the cross-linking of MDR3 with a thiol-reactive fluorophore blocked ATP hydrolysis and exhibited no PC stimulation. Similarly, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin lipids did not induce an increase of wild type MDR3 ATPase activity. The phosphate analogues beryllium fluoride and aluminum fluoride led to complete inhibition of ATPase activity, whereas orthovanadate inhibited exclusively the PC-stimulated ATPase activity of MDR3. The Q1174E mutation is located in the nucleotide-binding domain in direct proximity of the leucine of the ABC signature motif and extended the X loop, which is found in ABC exporters. Our data on the Q1174E mutant demonstrated basal ATPase activity, but PC lipids were incapable of stimulating ATPase activity highlighting the role of the extended X loop in the cross-talk of the nucleotide-binding domain and the transmembrane domain. PMID:25533467

  2. Weak operator binding enhances simulated Lac repressor-mediated DNA looping.

    PubMed

    Colasanti, Andrew V; Grosner, Michael A; Perez, Pamela J; Clauvelin, Nicolas; Lu, Xiang-Jun; Olson, Wilma K

    2013-12-01

    The 50th anniversary of Biopolymers coincides closely with the like celebration of the discovery of the Escherichia coli (lac) lactose operon, a classic genetic system long used to illustrate the influence of biomolecular structure on function. The looping of DNA induced by the binding of the Lac repressor protein to sequentially distant operator sites on DNA continues to serve as a paradigm for understanding long-range genomic communication. Advances in analyses of DNA structures and in incorporation of proteins in computer simulations of DNA looping allow us to address long-standing questions about the role of protein-mediated DNA loop formation in transcriptional control. Here we report insights gained from studies of the sequence-dependent contributions of the natural lac operators to Lac repressor-mediated DNA looping. Novel superposition of the ensembles of protein-bound operator structures derived from NMR measurements reveals variations in DNA folding missed in conventional structural alignments. The changes in folding affect the predicted ease with which the repressor induces loop formation and the ways that DNA closes between the protein headpieces. The peeling of the auxiliary operators away from the repressor enhances the formation of loops with the 92-bp wildtype spacing and hints of a structural reason behind their weak binding. PMID:23818216

  3. Rollercoaster loop shapes

    NASA Astrophysics Data System (ADS)

    Pendrill, Ann-Marie

    2005-11-01

    Many modern rollercoasters feature loops. Although textbook loops are often circular, real rollercoaster loops are not. In this paper, we look into the mathematical description of various possible loop shapes, as well as their riding properties. We also discuss how a study of loop shapes can be used in physics education.

  4. The loop structure and the RNA helicase p72/DDX17 influence the processing efficiency of the mice miR-132.

    PubMed

    Remenyi, Judit; Bajan, Sarah; Fuller-Pace, Frances V; Arthur, J Simon C; Hutvagner, Gyorgy

    2016-01-01

    miRNAs are small RNAs that are key regulators of gene expression in eukaryotic organisms. The processing of miRNAs is regulated by structural characteristics of the RNA and is also tightly controlled by auxiliary protein factors. Among them, RNA binding proteins play crucial roles to facilitate or inhibit miRNA maturation and can be controlled in a cell, tissue and species-specific manners or in response to environmental stimuli. In this study we dissect the molecular mechanism that promotes the overexpression of miR-132 in mice over its related, co-transcribed and co-regulated miRNA, miR-212. We have shown that the loop structure of miR-132 is a key determinant for its efficient processing in cells. We have also identified a range of RNA binding proteins that recognize the loop of miR-132 and influence both miR-132 and miR-212 processing. The DEAD box helicase p72/DDX17 was identified as a factor that facilitates the specific processing of miR-132. PMID:26947125

  5. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  6. Microwave Induced Structural Transitions in Polymers

    NASA Astrophysics Data System (ADS)

    Yang, Yuning; Lai, Wei-Chi

    2005-03-01

    Polymer chain dynamics as a function of temperature (in the range from 20 to 190 ^oC) have been studied using dielectric spectroscopy within the microwave frequency range. The frequency of radiation was varied from 0.5 GHz to 18 GHz. These studies were conducted for poly(caprolactone) (PCL), poly(ethylene oxide) (PEO), poly(vinyl acetate) (PvAC), poly(lactic acid), polystyrene (PS), nylon 6 and poly(methyl methacrylate) (PMMA). These polymers possess glass temperatures ranging from -- 62 ^oC (PCL) to 110 ^oC (PMMA). One broad relaxation process was found only for low Tg polymers (PCL and PEO) and not for the others. Results from temperature-dependent dielectric spectroscopy indicate that the relaxation process follows an Arrhenius T dependence suggesting the relaxation process is due to local motions. Moreover, the effect due to end groups was investigated by comparing results of PEO with hydroxy versus methoxy end groups. It was determined the structural transitions measured are not with end group motions. From the Debye diffusive model, the relaxation process is concluded to be associated with the short segmental motion along the backbone.

  7. Buckliballs: Buckling-Induced Pattern Transformation of Structured Elastic Shells

    NASA Astrophysics Data System (ADS)

    Bertoldi, Katia; Shim, Jongmin; Perdigou, Claude J.; Chen, Elizabeth R.; Reis, Pedro M.

    2012-02-01

    We present a class of continuum shell structures, the buckliball, which, undergo a structural transformation induced by buckling under pressure loading. The geometry of the buckliball comprises a spherical shell patterned with a regular array of circular voids. Moreover, we show that the buckling-induced pattern transformation is possible only with five specific hole arrangements. These voids are covered with a thin membrane, thereby making the ball air tight. Beyond a critical internal pressure, the thin ligaments between the voids buckle leading to a cooperative buckling cascade of the skeleton of the ball. Both precision desktop-scale experiments and finite element simulations are used to explore the underlying mechanics in detail and proof of concept of the proposed structures. We find excellent qualitative and quantitative agreement between experiments and simulations. This pattern transformation induced by a mechanical instability opens the possibility for reversible encapsulation, over a wide range of length scales.

  8. Thermally-induced structural motions of satellite solar arrays

    NASA Astrophysics Data System (ADS)

    Johnston, John Dennis

    1999-11-01

    Satellites have experienced attitude disturbances resulting from thermally. induced structural motions of flexible appendages since the early days of the space program. Thermally-induced structural motions are typically initiated during orbital eclipse transitions when a satellite exits from or enters into the Earth's shadow. The accompanying rapid changes in thermal loading may lead to time-varying temperature differences through the cross-section of appendages resulting in differential thermal expansion and corresponding structural deformations. Since the total angular momentum of the system must be conserved, motions of flexible appendages such as booms and solar arrays result in rigid body rotations of the entire satellite. These potentially large attitude disturbances may violate satellite pointing and jitter requirements. This research investigates thermally-induced structural motions of rigid panel solar arrays (solar panels) through analytical and experimental studies. Orbital eclipse transition heating and thermal analyses were completed to study solar panel thermal behavior and provide results for input to dynamics analyses. A hybrid coordinate dynamical model was utilized to study the planar dynamics of a simple satellite consisting of a rigid hub with a cantilevered flexible solar panel undergoing thermally-induced structural motions. Laboratory experimental studies were carried out to gain new insight into thermal-structural behavior and to validate analytical models. The experimental studies investigated the thermal-structural performance of honeycomb sandwich panels and satellite solar panel hardware subject to simulated eclipse transition heating. Results from the analytical and experimental studies illustrate the importance of the through-the-thickness temperature difference and its time derivatives as well as the ratio of the characteristic thermal and structural response times in solar panel thermally-induced structural motions. The thermal-structural

  9. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity.

    PubMed

    Manjasetty, Babu A; Halavaty, Andrei S; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol. PMID:26796657

  10. LeuO enhances butyrate-induced virulence expression through a positive regulatory loop in enterohaemorrhagic Escherichia coli.

    PubMed

    Takao, Miyuki; Yen, Hilo; Tobe, Toru

    2014-09-01

    Enterohaemorrhagic Escherichia coli (EHEC) causes bloody diarrhoea and other severe symptoms such as haemorrhagic uraemic syndrome. The expression of virulence genes on the locus for enterocyte effacement (LEE) and associated genes is regulated by a variety of factors, including transcriptional regulators and environmental signals. Butyrate, one of the major short-chain fatty acids present in the intestine, enhances expression of LEE genes and flagella biosynthesis genes in EHEC O157:H7, resulting in increased bacterial adherence and motility. Here, we show that expression of the leuO gene, which encodes a LysR-type transcriptional regulator, is enhanced by butyrate via Lrp, which is also necessary for butyrate-induced responses of LEE genes. LeuO expression induces prolonged activation of the promoter of LEE1 operon, including the ler gene, as well as virulence mechanisms such as microcolony formation. Activation of the LEE1 promoter by LeuO depends on another regulator, called Pch. The response of the leuO promoter to butyrate requires two virulence regulators, Pch and Ler, in addition to Lrp. Pch, Ler and Lrp bind the upstream region of the leuO promoter. Thus, leuO is involved in butyrate-enhanced expression of LEE genes through a positive feedback mechanism, but its expression and action on the LEE1 promoter are dependent on the virulence regulators Pch and Ler.

  11. Complete subsite mapping of a "loopful" GH19 chitinase from rye seeds based on its crystal structure.

    PubMed

    Ohnuma, Takayuki; Umemoto, Naoyuki; Kondo, Kaori; Numata, Tomoyuki; Fukamizo, Tamo

    2013-08-19

    Crystallographic analysis of a mutated form of "loopful" GH19 chitinase from rye seeds a double mutant RSC-c, in which Glu67 and Trp72 are mutated to glutamine and alanine, respectively, (RSC-c-E67Q/W72A) in complex with chitin tetrasaccharide (GlcNAc)₄ revealed that the entire substrate-binding cleft was completely occupied with the sugar residues of two (GlcNAc)₄ molecules. One (GlcNAc)₄ molecule bound to subsites -4 to -1, while the other bound to subsites +1 to +4. Comparisons of the main chain conformation between liganded RSC-c-E67Q/W72A and unliganded wild type RSC-c suggested domain motion essential for catalysis. This is the first report on the complete subsite mapping of GH19 chitinase.

  12. Water Stream "Loop-the-Loop"

    ERIC Educational Resources Information Center

    Jefimenko, Oleg

    1974-01-01

    Discusses the design of a modified loop-the-loop apparatus in which a water stream is used to illustrate centripetal forces and phenomena of high-velocity hydrodynamics. Included are some procedures of carrying out lecture demonstrations. (CC)

  13. Disruption of the 5' stem-loop of yeast U6 RNA induces trimethylguanosine capping of this RNA polymerase III transcript in vivo.

    PubMed Central

    Kwan, S; Gerlach, V L; Brow, D A

    2000-01-01

    Primary transcripts made by RNA polymerase II (Pol II), but not Pol I or Pol III, are modified by addition of a 7-methylguanosine (m7G) residue to the triphosphate 5' end shortly after it emerges from the polymerase. The m7G "caps" of small nuclear and small nucleolar RNAs, but not messenger RNAs, are subsequently hypermethylated to a 2,2,7-trimethylguanosine (TMG) residue. U6 RNA, the only small nuclear RNA synthesized by Pol III in most eukaryotes, does not receive a methylguanosine cap. However, human U6 RNA is O-methylated on the 5'-terminal (gamma) phosphate by an enzyme that recognizes the 5' stem-loop of U6. Here we show that variant yeast U6 RNAs truncated or substituted within the 5' stem-loop are TMG capped in vivo. Accumulation of the most efficiently TMG-capped U6 RNA variant is strongly inhibited by a conditional mutation in the largest subunit of Pol III, confirming that it is indeed synthesized by Pol III. Thus, methylguanosine capping and cap hypermethylation are not exclusive to Pol II transcripts in yeast. We propose that TMG capping of variant U6 RNAs occurs posttranscriptionally due to exposure of the 5' triphosphate by disruption of protein binding and/or gamma-methyl phosphate capping. 5' truncation and TMG capping of U6 RNA does not appear to affect its normal function in splicing, suggesting that assembly and action of the spliceosome is not very sensitive to the 5' end structure of U6 RNA. PMID:11142384

  14. Redesign of the Active Site of Sucrose Phosphorylase through a Clash-Induced Cascade of Loop Shifts.

    PubMed

    Kraus, Michael; Grimm, Clemens; Seibel, Jürgen

    2016-01-01

    Sucrose phosphorylases have been applied in the enzymatic production of glycosylated compounds for decades. However, several desirable acceptors, such as flavonoids or stilbenoids, that exhibit diverse antimicrobial, anticarcinogenic or antioxidant properties, remain poor substrates. The Q345F exchange in sucrose phosphorylase from Bifidobacterium adolescentis allows efficient glucosylation of resveratrol, (+)-catechin and (-)-epicatechin in yields of up to 97 % whereas the wild-type enzyme favours sucrose hydrolysis. Three previously undescribed products are made available. The crystal structure of the variant reveals a widened access channel with a hydrophobic aromatic surface that is likely to contribute to the improved activity towards aromatic acceptors. The generation of this channel can be explained in terms of a cascade of structural changes arising from the Q345F exchange. The observed mechanisms are likely to be relevant for the design of other tailor-made enzymes.

  15. Rogowski Loop design for NSTX

    SciTech Connect

    McCormack, B.; Kaita, R.; Kugel, H.; Hatcher, R.

    2000-01-06

    The Rogowski Loop is one of the most basic diagnostics for tokamak operations. On the National Spherical Torus Experiment (NSTX), the plasma current Rogowski Loop had the constraints of the very limited space available on the center stack, 5,000 volt isolation, flexibility requirements as it remained a part of the Center Stack assembly after the first phase of operation, and a +120 C temperature requirement. For the second phase of operation, four Halo Current Rogowski Loops under the Center Stack tiles will be installed having +600 C and limited space requirements. Also as part of the second operational phase, up to ten Rogowski Loops will installed to measure eddy currents in the Passive Plate support structures with +350 C, restricted space, and flexibility requirements. This presentation will provide the details of the material selection, fabrication techniques, testing, and installation results of the Rogowski Loops that were fabricated for the high temperature operational and bakeout requirements, high voltage isolation requirements, and the space and flexibility requirements imposed upon the Rogowski Loops. In the future operational phases of NSTX, additional Rogowski Loops could be anticipated that will measure toroidal plasma currents in the vacuum vessel and in the Passive Plate assemblies.

  16. Observations of loops and prominences

    NASA Technical Reports Server (NTRS)

    Strong, Keith T.

    1994-01-01

    We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly

  17. All three Ca[superscript 2+]-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin

    SciTech Connect

    Deng, Lu; Vysotski, Eugene S.; Markova, Svetlana V.; Liu, Zhi-Jie; Lee, John; Rose, John; Wang, Bi-Cheng

    2010-07-13

    The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 {angstrom} and 2.2 {angstrom}, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca{sup 2+}-discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca{sup 2+} concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.

  18. Crystal structure of laser-induced subsurface modifications in Si

    DOE PAGESBeta

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in ’t Veld, A. J.

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystalmore » structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.« less

  19. Crystal structure of laser-induced subsurface modifications in Si

    SciTech Connect

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in ’t Veld, A. J.

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.

  20. Basic helix-loop-helix transcription factor DEC1 regulates the cisplatin-induced apoptotic pathway of human esophageal cancer cells.

    PubMed

    Seino, Hiroko; Wu, Yunyan; Morohashi, Satoko; Kawamoto, Takeshi; Fujimoto, Katsumi; Kato, Yukio; Takai, Yoshihiro; Kijima, Hiroshi

    2015-01-01

    DEC1 [basic helix-loop-helix (BHLH) E40/Stra13/Sharp2] and DEC2 (BHLHE41/Sharp1) are BHLH transcription factors that are associated with the regulation of apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. However, the roles of DEC1 and DEC2 expression in esophageal cancer are poorly understood. In this study, we examined the roles of DEC1 and DEC2 in human esophageal cancer TE 5 and TE 10 cells that had been treated with cis-diamminedichloroplatinum (II) (cisplatin: CDDP). Expression of DEC1 and DEC2 was decreased with CDDP treatment in TE 5 cells; however, knockdown or overexpression of DEC1/DEC2 had little effects on CDDP-induced apoptosis in TE 5 cells. DEC1 expression was up-regulated in CDDP-treated TE 10 cells, whereas DEC2 expression was unchanged. DEC1 knockdown by siRNA in TE 10 decreased the amount of cleaved poly (ADP-ribose) polymerase (PARP) after treatment with CDDP, whereas DEC2 knockdown had no effects on the amount of cleaved PARP in both the presence and absence of CDDP. We also demonstrated that DEC1 overexpression promoted cleaved PARP expression, whereas DEC2 overexpression had no effects on the amount of cleaved PARP in TE 10 cells. These results suggested that DEC1 has pro-apoptotic effects on human esophageal cancer TE 10 cells of well-differentiated type.

  1. Capsaicin-Induced Activation of p53-SMAR1 Auto-Regulatory Loop Down-Regulates VEGF in Non-Small Cell Lung Cancer to Restrain Angiogenesis

    PubMed Central

    Chakraborty, Samik; Mukherjee, Shravanti; Bhattacharjee, Pushpak; Guha, Deblina; Choudhuri, Tathagata; Chattopadhyay, Samit; Sa, Gaurisankar; Sen, Aparna; Das, Tanya

    2014-01-01

    Lung cancer is the leading cause of cancer-related deaths worldwide. Despite decades of research, the treatment options for lung cancer patients remain inadequate, either to offer a cure or even a substantial survival advantage owing to its intrinsic resistance to chemotherapy. Our results propose the effectiveness of capsaicin in down-regulating VEGF expression in non-small cell lung carcinoma (NSCLC) cells in hypoxic environment. Capsaicin-treatment re-activated p53-SMAR1 positive feed-back loop in these cells to persuade p53-mediated HIF-1α degradation and SMAR1-induced repression of Cox-2 expression that restrained HIF-1α nuclear localization. Such signal-modulations consequently down regulated VEGF expression to thwart endothelial cell migration and network formation, pre-requisites of angiogenesis in tumor micro-environment. The above results advocate the candidature of capsaicin in exclusively targeting angiogenesis by down-regulating VEGF in tumor cells to achieve more efficient and cogent therapy of resistant NSCLC. PMID:24926985

  2. The kissing-loop T-shaped structure translational enhancer of Pea enation mosaic virus can bind simultaneously to ribosomes and a 5' proximal hairpin.

    PubMed

    Gao, Feng; Gulay, Suna P; Kasprzak, Wojciech; Dinman, Jonathan D; Shapiro, Bruce A; Simon, Anne E

    2013-11-01

    The Pea enation mosaic virus (PEMV) 3' translational enhancer, known as the kissing-loop T-shaped structure (kl-TSS), binds to 40S subunits, 60S subunits, and 80S ribosomes, whereas the Turnip crinkle virus (TCV) TSS binds only to 60S subunits and 80S ribosomes. Using electrophoretic mobility gel shift assay (EMSA)-based competition assays, the kl-TSS was found to occupy a different site in the ribosome than the P-site-binding TCV TSS, suggesting that these two TSS employ different mechanisms for enhancing translation. The kl-TSS also engages in a stable, long-distance RNA-RNA kissing-loop interaction with a 12-bp 5'-coding-region hairpin that does not alter the structure of the kl-TSS as revealed by molecular dynamics simulations. Addition of the kl-TSS in trans to a luciferase reporter construct containing either wild-type or mutant 5' and 3' PEMV sequences suppressed translation, suggesting that the kl-TSS is required in cis to function, and both ribosome-binding and RNA interaction activities of the kl-TSS contributed to translational inhibition. Addition of the kl-TSS was more detrimental for translation than an adjacent eIF4E-binding 3' translational enhancer known as the PTE, suggesting that the PTE may support the ribosome-binding function of the kl-TSS. Results of in-line RNA structure probing, ribosome filter binding, and high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE) of rRNAs within bound ribosomes suggest that kl-TSS binding to ribosomes and binding to the 5' hairpin are compatible activities. These results suggest a model whereby posttermination ribosomes/ribosomal subunits bind to the kl-TSS and are delivered to the 5' end of the genome via the associated RNA-RNA interaction, which enhances the rate of translation reinitiation.

  3. Exploring the conformational diversity of loops on conserved frameworks.

    PubMed

    Li, W; Liang, S; Wang, R; Lai, L; Han, Y

    1999-12-01

    Loops are structurally variable regions, but the secondary structural elements bracing loops are often conserved. Motifs with similar secondary structures exist in the same and different protein families. In this study, we made an all-PDB-based analysis and produced 495 motif families accessible from the Internet. Every motif family contains some variable loops spanning a common framework (a pair of secondary structures). The diversity of loops and the convergence of frameworks were examined. In addition, we also identified 119 loops with conformational changes in different PDB files. These materials can give some directions for functional loop design and flexible docking. PMID:10611401

  4. A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem.

    PubMed Central

    de Bruijn, M H; Klug, A

    1983-01-01

    The mammalian mitochondrial tRNA(AGY)Ser is unique in lacking the entire dihydrouridine arm. This reduces its secondary structure to a 'truncated cloverleaf'. Experimental evidence on the tertiary structure has been obtained by chemically probing the conformation of both the bovine and human species in their native conformation and at various stages of denaturation. A structural model of the bovine tRNA is presented based on the results of this chemical probing, on a comparison between nine homologous 'truncated cloverleaf' secondary structures and on analogies with the crystal structure of yeast phenylalanine tRNA. The proposed structure is very similar in shape to that of yeast tRNA(Phe) but is slightly smaller in size. It is defined by a unique set of tertiary interactions. Structural considerations suggest that other mammalian mitochondrial tRNAs have smaller dimensions as well. Images Fig. 1. Fig. 1. Fig. 1. Fig. 3. PMID:10872325

  5. Green tea (Camellia sinensis) alleviates arsenic-induced damages to DNA and intestinal tissues in rat and in situ intestinal loop by reinforcing antioxidant system.

    PubMed

    Acharyya, Nirmallya; Sajed Ali, Sk; Deb, Bimal; Chattopadhyay, Sandip; Maiti, Smarajit

    2015-09-01

    This study elucidates the protective role of Green tea (Camellia sinensis or CS) against arsenic-induced mutagenic DNA-breakage/intestinal (small) damages in female rats. Intestinal epithelial cells receive ingested arsenic initially. Though, the possibility of damages in this tissue is immense and the therapeutic strategies against this damage are of great concern, reports on either issue are scanty. Our earlier study on arsenic-exposed human unveils a link between carcinogenesis and mutagenic DNA damage. Here, we demonstrate that supplementation of CS-extract (10 mg/mL water) with NaAsO2 (0.6 ppm)/100 g b.w. for 28 days to rats offered a significant protection against arsenic-induced oxidative damages to DNA and intestinal (small) tissues by buttressing antioxidant systems. Necrotic and apoptotic damages and their CS-protection are shown in DNA-fragmentation, comet-assay, and histoarchitecture (hematoxylin and eosin and periodic acid-schiff staining) results. Only arsenic exposure significantly decreased intestinal superoxide dismutase, catalase activities, and level of soluble thiol with a concomitant increase in malondialdehyde/conjugated dienes. Alteration of serum necrotic marker lactate dehydrogenase and the metabolic inflammatory marker c-reactive protein also indicate the impairment may be occurring at transcription and/or cellular signal transduction level. In addition, in situ incubation in rat intestinal loop filled for 24 h with NaAsO2 alone (250 µM) or with aqueous CS-extract (250 mg/mL) suggests that small intestinal epithelial cells are significantly protected by CS against arsenic-associated necrotic/mutagenic damages, which is observed in DNA-breakage studies. In conclusion, besides intensifying endogenous antioxidant system, CS polyphenols also offer a direct role on free radical scavenging activity that is associated to the protection from mutagenic DNA-breakages and prevention of tissue necrosis/carcinogenesis generated by arsenic.

  6. Fiber Loop Ringdown Sensor for Potential Real-Time Monitoring of Cracks in Concrete Structures: An Exploratory Study

    PubMed Central

    Sahay, Peeyush; Kaya, Malik; Wang, Chuji

    2013-01-01

    A fiber loop ringdown (FLRD) concrete crack sensor is described for the first time. A bare single mode fiber (SMF), without using other optical components or chemical coatings, etc., was utilized to construct the sensor head, which was driven by a FLRD sensor system. The performance of the sensor was evaluated on concrete bars with dimensions 20 cm × 5 cm × 5 cm, made in our laboratory. Cracks were produced manually and the responses of the sensor were recorded in terms of ringdown times. The sensor demonstrated detection of the surface crack width (SCW) of 0.5 mm, which leads to a theoretical SCW detection limit of 31 μm. The sensor's response to a cracking event is near real-time (1.5 s). A large dynamic range of crack detection ranging from a few microns (μm) to a few millimeters is expected from this sensor. With the distinct features, such as simplicity, temperature independence, near real-time response, high SCW detection sensitivity, and a large dynamic range, this FLRD crack sensor appears promising for detections of cracks when embedded in concrete. PMID:23344372

  7. Shear-Induced Structural and Morphological Changes in Polyolefin Blends

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Kim, Hongdoo; Hobbie, Erik K.; Wang, Zhi-Gang; Katsumi, Shimizu; Han, Charles C.; Hsiao, Benjamin S.

    2002-03-01

    Shear-induced structural and morphological changes in blends of statistical copolymers of ethylene/hexene (PEH) and ethylene/butene (PEB) have been investigated using both scattering and real-space imaging techniques. In a blend where the minority PEH forms crystallite suspensions, small angle laser light scattering and phase contrast optical microscopy reveal unusual morphological changes with increasing shear rate. At low shear rates, anisotropic crystallite superstructures orient with flow; at higher shear rates, orientation at the lamellar level is seen; at even higher shear rates, significant shear melting occurs, while the remaining aggregates to form necklace structures. Synchrotron X-ray scattering reveals that polymer chains align following a step-shear, with the lamella then growing anisotropically. Transmission electron microscopy reveals details of the shear-induced structure. Possible mechanisms will be discussed.

  8. Strain-induced ultrahard and ultrastable nanolaminated structure in nickel.

    PubMed

    Liu, X C; Zhang, H W; Lu, K

    2013-10-18

    Heavy plastic deformation may refine grains of metals and make them very strong. But the strain-induced refinement saturates at large strains, forming three-dimensional ultrafine-grained (3D UFG) structures with random orientations. Further refinement of this microstructure is limited because of the enhanced mobility of grain boundaries. Very-high-rate shear deformation with high strain gradients was applied in the top surface layer of bulk nickel, where a 2D nanometer-scale laminated structure was induced. The strongly textured nanolaminated structure (average lamellar thickness of 20 nanometers) with low-angle boundaries among the lamellae is ultrahard and ultrastable: It exhibits a hardness of 6.4 gigapascal--which is higher than any reported hardness of the UFG nickel--and a coarsening temperature of 40 kelvin above that in UFG nickel. PMID:24136963

  9. Behavior control in the sensorimotor loop with short-term synaptic dynamics induced by self-regulating neurons.

    PubMed

    Toutounji, Hazem; Pasemann, Frank

    2014-01-01

    The behavior and skills of living systems depend on the distributed control provided by specialized and highly recurrent neural networks. Learning and memory in these systems is mediated by a set of adaptation mechanisms, known collectively as neuronal plasticity. Translating principles of recurrent neural control and plasticity to artificial agents has seen major strides, but is usually hampered by the complex interactions between the agent's body and its environment. One of the important standing issues is for the agent to support multiple stable states of behavior, so that its behavioral repertoire matches the requirements imposed by these interactions. The agent also must have the capacity to switch between these states in time scales that are comparable to those by which sensory stimulation varies. Achieving this requires a mechanism of short-term memory that allows the neurocontroller to keep track of the recent history of its input, which finds its biological counterpart in short-term synaptic plasticity. This issue is approached here by deriving synaptic dynamics in recurrent neural networks. Neurons are introduced as self-regulating units with a rich repertoire of dynamics. They exhibit homeostatic properties for certain parameter domains, which result in a set of stable states and the required short-term memory. They can also operate as oscillators, which allow them to surpass the level of activity imposed by their homeostatic operation conditions. Neural systems endowed with the derived synaptic dynamics can be utilized for the neural behavior control of autonomous mobile agents. The resulting behavior depends also on the underlying network structure, which is either engineered or developed by evolutionary techniques. The effectiveness of these self-regulating units is demonstrated by controlling locomotion of a hexapod with 18 degrees of freedom, and obstacle-avoidance of a wheel-driven robot. PMID:24904403

  10. Behavior control in the sensorimotor loop with short-term synaptic dynamics induced by self-regulating neurons

    PubMed Central

    Toutounji, Hazem; Pasemann, Frank

    2014-01-01

    The behavior and skills of living systems depend on the distributed control provided by specialized and highly recurrent neural networks. Learning and memory in these systems is mediated by a set of adaptation mechanisms, known collectively as neuronal plasticity. Translating principles of recurrent neural control and plasticity to artificial agents has seen major strides, but is usually hampered by the complex interactions between the agent's body and its environment. One of the important standing issues is for the agent to support multiple stable states of behavior, so that its behavioral repertoire matches the requirements imposed by these interactions. The agent also must have the capacity to switch between these states in time scales that are comparable to those by which sensory stimulation varies. Achieving this requires a mechanism of short-term memory that allows the neurocontroller to keep track of the recent history of its input, which finds its biological counterpart in short-term synaptic plasticity. This issue is approached here by deriving synaptic dynamics in recurrent neural networks. Neurons are introduced as self-regulating units with a rich repertoire of dynamics. They exhibit homeostatic properties for certain parameter domains, which result in a set of stable states and the required short-term memory. They can also operate as oscillators, which allow them to surpass the level of activity imposed by their homeostatic operation conditions. Neural systems endowed with the derived synaptic dynamics can be utilized for the neural behavior control of autonomous mobile agents. The resulting behavior depends also on the underlying network structure, which is either engineered or developed by evolutionary techniques. The effectiveness of these self-regulating units is demonstrated by controlling locomotion of a hexapod with 18 degrees of freedom, and obstacle-avoidance of a wheel-driven robot. PMID:24904403

  11. Crystal structures of SIRT3 reveal that the α2-α3 loop and α3-helix affect the interaction with long-chain acyl lysine.

    PubMed

    Gai, Wei; Li, He; Jiang, Hualiang; Long, Yaqiu; Liu, Dongxiang

    2016-09-01

    SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study the binding modes of sirtuins to long-chain acyl lysines, we solved the crystal structures of SIRT3 bound to either a H3K9-myristoylated- or a H3K9-palmitoylated peptide. Interaction of SIRT3 with the palmitoyl group led to unfolding of the α3-helix. The myristoyl and palmitoyl groups bind to the C-pocket and an allosteric site near the α3-helix, respectively. We found that the residues preceding the α3-helix determine the size of the C-pocket. The flexibility of the α2-α3 loop and the plasticity of the α3-helix affect the interaction with long-chain acyl lysine. PMID:27501476

  12. Look before You Loop.

    ERIC Educational Resources Information Center

    Bellis, Marilyn

    1999-01-01

    Explores looping, which involves one teacher staying with the same group of children for more than one year. Recognizes that, with today's changing demographics, looping can be a way to foster a family-like classroom atmosphere. Discusses advantages and disadvantages to looping. Includes a chart of looping opportunities and considerations;…

  13. Leukocyte integrin αLβ2 headpiece structures: The αI domain, the pocket for the internal ligand, and concerted movements of its loops.

    PubMed

    Sen, Mehmet; Springer, Timothy A

    2016-03-15

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.

  14. Fast flux locked loop

    DOEpatents

    Ganther, Jr., Kenneth R.; Snapp, Lowell D.

    2002-09-10

    A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

  15. OPE for super loops

    NASA Astrophysics Data System (ADS)

    Sever, Amit; Vieira, Pedro; Wang, Tianheng

    2011-11-01

    We extend the Operator Product Expansion for Null Polygon Wilson loops to the Mason-Skinner-Caron-Huot super loop dual to non MHV gluon amplitudes. We explain how the known tree level amplitudes can be promoted into an infinite amount of data at any loop order in the OPE picture. As an application, we re-derive all one loop NMHV six gluon amplitudes by promoting their tree level expressions. We also present some new all loops predictions for these amplitudes.

  16. The preprocessed doacross loop

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi

    1990-01-01

    Dependencies between loop iterations cannot always be characterized during program compilation. Doacross loops typically make use of a-priori knowledge of inter-iteration dependencies to carry out required synchronizations. A type of doacross loop is proposed that allows the scheduling of iterations of a loop among processors without advance knowledge of inter-iteration dependencies. The method proposed for loop iterations requires that parallelizable preprocessing and postprocessing steps be carried out during program execution.

  17. Effects of mutations in stem and loop regions on the structure and function of adenovirus VA RNAI.

    PubMed Central

    Mellits, K H; Mathews, M B

    1988-01-01

    Adenovirus virus-associated (VA) RNAI is required for efficient protein synthesis at late times of adenoviral infection, and in some other situations where double-stranded RNA (dsRNA) is present. It prevents inhibition of protein synthesis by a dsRNA-activated protein kinase and the secondary structure of VA RNAI is though to be important for its activity. To test this idea and to define structures and sequences responsible for VA RNAI activity, we constructed several mutant VA RNA genes and tested them in a transient expression assay. Activity is unaffected by deletions within a small region near the center of the gene, nt 72-85, but it is greatly diminished by deletion or substitution of sequences on the 3' side of this region. The structures of wild-type and mutant RNAs were examined by nuclease-sensitivity analysis. We propose a model for wild-type VA RNAI which differs from that predicted to be the most stable structure. Surprisingly disruption of the longest duplex region in the molecule is tolerated, provided that adjacent structural elements are not rearranged. However, perturbations of elements located in the center of the structure correlate well with loss of function. Images PMID:3181142

  18. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles).

    PubMed

    Bhattacharyya, A; Lilley, D M

    1989-09-12

    We have studied the structure and reactivities of two kinds of mismatched DNA sequences--unopposed bases, or bulges, and multiple mismatched pairs of bases. These were generated in a constant sequence environment, in relatively long DNA fragments, using a technique based on heteroduplex formation between sequences cloned into single-stranded M13 phage. The mismatched sequences were studied from two points of view, viz 1. The mobility of the fragments on gel electrophoresis in polyacrylamide was studied in order to examine possible bending of the DNA due to the presence of the mismatch defect. Such bending would constitute a global effect on the conformation of the molecule. 2. Sequences in and around the mismatches were studied using enzyme and chemical probes of DNA structure. This would reveal more local structural effects of the mismatched sequences. We observed that the structures of the bulges and the multiple mismatches appear to be fundamentally different. The bulged sequences exhibited a large gel retardation, consistent with a significant bending of the DNA at the bulge, and whose magnitude depends on the number of mismatched bases. The larger bulges were sensitive to cleavage by single-strand specific nucleases, and modified by diethyl pyrocarbonate (adenines) or osmium tetroxide (thymines) in a non-uniform way, suggesting that the bulges have a precise structure that leads to exposure of some, but not all, of the bases. In contrast the multiple mismatches ('bubbles') cause very much less bending of the DNA fragment in which they occur, and uniform patterns of chemical reactivity along the length of the mismatched sequences, suggesting a less well defined, and possibly flexible, structure. The precise structure of the bulges suggests that such features may be especially significant for recognition by proteins.

  19. Support Substructures: Support-Induced Part-Level Structural Representation.

    PubMed

    Huang, Shi-Sheng; Fu, Hongbo; Wei, Ling-Yu; Hu, Shi-Min

    2016-08-01

    In this work we explore a support-induced structural organization of object parts. We introduce the concept of support substructures, which are special subsets of object parts with support and stability. A bottom-up approach is proposed to identify such substructures in a support relation graph. We apply the derived high-level substructures to part-based shape reshuffling between models, resulting in nontrivial functionally plausible model variations that are difficult to achieve with symmetry-induced substructures by the state-of-the-art methods. We also show how to automatically or interactively turn a single input model to new functionally plausible shapes by structure rearrangement and synthesis, enabled by support substructures. To the best of our knowledge no single existing method has been designed for all these applications. PMID:26336128

  20. Light-induced structural changes in a monomeric bacteriophytochrome.

    PubMed

    Takala, Heikki; Niebling, Stephan; Berntsson, Oskar; Björling, Alexander; Lehtivuori, Heli; Häkkänen, Heikki; Panman, Matthijs; Gustavsson, Emil; Hoernke, Maria; Newby, Gemma; Zontone, Federico; Wulff, Michael; Menzel, Andreas; Ihalainen, Janne A; Westenhoff, Sebastian

    2016-09-01

    Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. PMID:27679804

  1. Light-induced structural changes in a monomeric bacteriophytochrome

    PubMed Central

    Takala, Heikki; Niebling, Stephan; Berntsson, Oskar; Björling, Alexander; Lehtivuori, Heli; Häkkänen, Heikki; Panman, Matthijs; Gustavsson, Emil; Hoernke, Maria; Newby, Gemma; Zontone, Federico; Wulff, Michael; Menzel, Andreas; Ihalainen, Janne A.; Westenhoff, Sebastian

    2016-01-01

    Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes.

  2. Light-induced structural changes in a monomeric bacteriophytochrome

    PubMed Central

    Takala, Heikki; Niebling, Stephan; Berntsson, Oskar; Björling, Alexander; Lehtivuori, Heli; Häkkänen, Heikki; Panman, Matthijs; Gustavsson, Emil; Hoernke, Maria; Newby, Gemma; Zontone, Federico; Wulff, Michael; Menzel, Andreas; Ihalainen, Janne A.; Westenhoff, Sebastian

    2016-01-01

    Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. PMID:27679804

  3. A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch.

    PubMed

    Amacher, Jeanine F; Zhong, Fangfang; Lisi, George P; Zhu, Michael Q; Alden, Stephanie L; Hoke, Kevin R; Madden, Dean R; Pletneva, Ekaterina V

    2015-07-01

    It has been suggested that the alkaline form of cytochrome c (cyt c) regulates function of this protein as an electron carrier in oxidative phosphorylation and as a peroxidase that reacts with cardiolipin (CL) during apoptosis. In this form, Met80, the native ligand to the heme iron, is replaced by a Lys. While it has become clear that the structure of cyt c changes, the extent and sequence of conformational rearrangements associated with this ligand replacement remain a subject of debate. Herein we report a high-resolution crystal structure of a Lys73-ligated cyt c conformation that reveals intricate change in the heme environment upon this switch in the heme iron ligation. The structure is surprisingly compact, and the heme coordination loop refolds into a β-hairpin with a turn formed by the highly conserved residues Pro76 and Gly77. Repositioning of residue 78 modifies the intraprotein hydrogen-bonding network and, together with adjustments of residues 52 and 74, increases the volume of the heme pocket to allow for insertion of one of the CL acyl moieties next to Asn52. Derivatization of Cys78 with maleimide creates a solution mimic of the Lys-ligated cyt c that has enhanced peroxidase activity, adding support for a role of the Lys-ligated cyt c in the apoptotic mechanism. Experiments with the heme peptide microperoxidase-8 and engineered model proteins provide a thermodynamic rationale for the switch to Lys ligation upon perturbations in the protein scaffold. PMID:26038984

  4. EUV SPECTRAL LINE FORMATION AND THE TEMPERATURE STRUCTURE OF ACTIVE REGION FAN LOOPS: OBSERVATIONS WITH HINODE/EIS AND SDO/AIA

    SciTech Connect

    Brooks, David H.; Young, Peter R.; Warren, Harry P.

    2011-04-01

    With the aim of studying active region fan loops using observations from the Hinode EUV Imaging Spectrometer (EIS) and Solar Dynamics Observatory Atmospheric Imaging Assembly (AIA), we investigate a number of inconsistencies in modeling the absolute intensities of Fe VIII and Si VII lines, and address why spectroheliograms formed from these lines look very similar despite the fact that ionization equilibrium calculations suggest that they have significantly different formation temperatures: log(T{sub e} /K) = 5.6 and 5.8, respectively. It is important to resolve these issues because confidence has been undermined in their use for differential emission measure (DEM) analysis, and Fe VIII is the main contributor to the AIA 131 A channel at low temperatures. Furthermore, the strong Fe VIII 185.213 A and Si VII 275.368 A lines are the best EIS lines to use for velocity studies in the transition region, and for assigning the correct temperature to velocity measurements in the fans. We find that the Fe VIII 185.213 A line is particularly sensitive to the slope of the DEM, leading to disproportionate changes in its effective formation temperature. If the DEM has a steep gradient in the log(T{sub e} /K) = 5.6-5.8 temperature range, or is strongly peaked, Fe VIII 185.213 A and Si VII 275.368 A will be formed at the same temperature. We show that this effect explains the similarity of these images in the fans. Furthermore, we show that the most recent ionization balance compilations resolve the discrepancies in absolute intensities. With these difficulties overcome, we combine EIS and AIA data to determine the temperature structure of a number of fan loops and find that they have peak temperatures of 0.8-1.2 MK. The EIS data indicate that the temperature distribution has a finite (but narrow) width < log ({sigma}{sub Te}/K) = 5.5 which, in one detailed case, is found to broaden substantially toward the loop base. AIA and EIS yield similar results on the temperature, emission

  5. Chelation-Induced Polymer Structural Hierarchy/Complexity in Water.

    PubMed

    Han, Jie; Zhou, Kaiyi; Zhu, Xuechao; Yu, Qiuping; Ding, Yi; Lu, Xinhua; Cai, Yuanli

    2016-08-01

    Understanding nanoscale structural hierarchy/complexity of hydrophilic flexible polymers is imperative because it can be viewed as an analogue to protein-alike superstructures. However, current understanding is still in infancy. Herein the first demonstration of nanoscale structural hierarchy/complexity via copper chelation-induced self-assembly (CCISA) is presented. Hierarchically-ordered colloidal networks and disks can be achieved by deliberate control of spacer length and solution pH. Dynamic light scattering, transmission electron microscopy, and atomic force microscopy demonstrate that CCISA underwent supramolecular-to-supracolloidal stepwise-growth mechanism, and underline amazing prospects to the hierarchically-ordered superstructures of hydrophilic flexible polymers in water.

  6. Shear Induced Structural Relaxation in a Supercooled Colloidal Liquid

    NASA Astrophysics Data System (ADS)

    Chen, Dandan; Semwogerere, Denis; Weeks, Eric R.

    2009-11-01

    Amorphous materials include many common products we use everyday, such as window glass, moisturizer, shaving cream and peanut butter. These materials have liquid-like disordered structure, but keep their shapes like a solid. The rheology of dense amorphous materials under large shear strain is not fully understood, partly due to the difficulty of directly viewing the microscopic details of such materials. We use a colloidal suspension to simulate amorphous materials, and study the shear- induced structural relaxation with fast confocal microscopy. We quantify the plastic rearrangements of the particles using standard analysis techniques based on the motion of the particles.

  7. Gravitationally induced particle production and its impact on structure formation

    NASA Astrophysics Data System (ADS)

    Nunes, Rafael C.

    2016-08-01

    In this paper we investigate the influence of a continuous particles creation processes on the linear and nonlinear matter clustering, and its consequences on the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole l, showing that the scale where the nonlinear growth overcomes the linear effect depends strongly of particles creation rate.

  8. Dynamics of femtosecond laser induced voidlike structures in fused silica

    SciTech Connect

    Mermillod-Blondin, A.; Bonse, J.; Rosenfeld, A.; Hertel, I. V.; Meshcheryakov, Yu. P.; Bulgakova, N. M.; Audouard, E.; Stoian, R.

    2009-01-26

    Focused ultrafast laser irradiation of fused silica usually induces a spatially modulated refractive index variation in the bulk material. Strong energy concentration leads to the localized formation of a lower-density cavitylike depressed structure surrounded by compacted matter. We report on applying time-resolved phase contrast microscopy to investigate the timescale of the void formation. We indicate a temporal behavior consistent with shock wave generation and subsequent rarefaction.

  9. Run-time parallelization and scheduling of loops

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

    1990-01-01

    Run time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases, where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run time, wave fronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run time reordering of loop indices can have a significant impact on performance. Furthermore, the overheads associated with this type of reordering are amortized when the loop is executed several times with the same dependency structure.

  10. Buckling-induced encapsulation of structured elastic shells under pressure

    PubMed Central

    Shim, Jongmin; Perdigou, Claude; Chen, Elizabeth R.; Bertoldi, Katia; Reis, Pedro M.

    2012-01-01

    We introduce a class of continuum shell structures, the Buckliball, which undergoes a structural transformation induced by buckling under pressure loading. The geometry of the Buckliball comprises a spherical shell patterned with a regular array of circular voids. In order for the pattern transformation to be induced by buckling, the possible number and arrangement of these voids are found to be restricted to five specific configurations. Below a critical internal pressure, the narrow ligaments between the voids buckle, leading to a cooperative buckling cascade of the skeleton of the ball. This ligament buckling leads to closure of the voids and a reduction of the total volume of the shell by up to 54%, while remaining spherical, thereby opening the possibility of encapsulation. We use a combination of precision desktop-scale experiments, finite element simulations, and scaling analyses to explore the underlying mechanics of these foldable structures, finding excellent qualitative and quantitative agreement. Given that this folding mechanism is induced by a mechanical instability, our Buckliball opens the possibility for reversible encapsulation, over a wide range of length scales. PMID:22451901

  11. Predictive lethal proarrhythmic risk evaluation using a closed-loop-circuit cell network with human induced pluripotent stem cells derived cardiomyocytes

    NASA Astrophysics Data System (ADS)

    Nomura, Fumimasa; Hattori, Akihiro; Terazono, Hideyuki; Kim, Hyonchol; Odaka, Masao; Sugio, Yoshihiro; Yasuda, Kenji

    2016-06-01

    For the prediction of lethal arrhythmia occurrence caused by abnormality of cell-to-cell conduction, we have developed a next-generation in vitro cell-to-cell conduction assay, i.e., a quasi in vivo assay, in which the change in spatial cell-to-cell conduction is quantitatively evaluated from the change in waveforms of the convoluted electrophysiological signals from lined-up cardiomyocytes on a single closed loop of a microelectrode of 1 mm diameter and 20 µm width in a cultivation chip. To evaluate the importance of the closed-loop arrangement of cardiomyocytes for prediction, we compared the change in waveforms of convoluted signals of the responses in the closed-loop circuit arrangement with that of the response of cardiomyocyte clusters using a typical human ether a go-go related gene (hERG) ion channel blocker, E-4031. The results showed that (1) waveform prolongation and fluctuation both in the closed loops and clusters increased depending on the E-4031 concentration increase. However, (2) only the waveform signals in closed loops showed an apparent temporal change in waveforms from ventricular tachycardia (VT) to ventricular fibrillation (VF), which is similar to the most typical cell-to-cell conductance abnormality. The results indicated the usefulness of convoluted waveform signals of a closed-loop cell network for acquiring reproducible results acquisition and more detailed temporal information on cell-to-cell conduction.

  12. The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin

    PubMed Central

    Gao, Feng; Gulay, Suna P.; Kasprzak, Wojciech; Dinman, Jonathan D.

    2013-01-01

    The Pea Enation Mosaic Virus (PEMV) 3′ translational enhancer, known as the kissing-loop T-shaped structure (kl-TSS), binds to 40S subunits, 60S subunits, and 80S ribosomes, whereas the Turnip crinkle virus (TCV) TSS binds only to 60S subunits and 80S ribosomes. Using electrophoretic mobility gel shift assay (EMSA)-based competition assays, the kl-TSS was found to occupy a different site in the ribosome than the P-site-binding TCV TSS, suggesting that these two TSS employ different mechanisms for enhancing translation. The kl-TSS also engages in a stable, long-distance RNA-RNA kissing-loop interaction with a 12-bp 5′-coding-region hairpin that does not alter the structure of the kl-TSS as revealed by molecular dynamics simulations. Addition of the kl-TSS in trans to a luciferase reporter construct containing either wild-type or mutant 5′ and 3′ PEMV sequences suppressed translation, suggesting that the kl-TSS is required in cis to function, and both ribosome-binding and RNA interaction activities of the kl-TSS contributed to translational inhibition. Addition of the kl-TSS was more detrimental for translation than an adjacent eIF4E-binding 3′ translational enhancer known as the PTE, suggesting that the PTE may support the ribosome-binding function of the kl-TSS. Results of in-line RNA structure probing, ribosome filter binding, and high-throughput selective 2′-hydroxyl acylation analyzed by primer extension (hSHAPE) of rRNAs within bound ribosomes suggest that kl-TSS binding to ribosomes and binding to the 5′ hairpin are compatible activities. These results suggest a model whereby posttermination ribosomes/ribosomal subunits bind to the kl-TSS and are delivered to the 5′ end of the genome via the associated RNA-RNA interaction, which enhances the rate of translation reinitiation. PMID:23986599

  13. Non-enzymatic glycation induces structural modifications of myoglobin.

    PubMed

    Roy, Anjana; Sil, Rajarshi; Chakraborti, Abhay Sankar

    2010-05-01

    Increased glucose concentration in diabetes mellitus causes glycation of several proteins, leading to changes in their properties. Although glycation-induced functional modification of myoglobin is known, structural modification of the protein has not yet been reported. Here, we have studied glucose-modified structural changes of the heme protein. After in vitro glycation of metmyoglobin (Mb) by glucose at 25 degrees C for 6 days, glycated myoglobin (GMb) and unchanged Mb have been separated by ion exchange (BioRex 70) chromatography, and their properties have been compared. Compared to Mb, GMb exhibits increased absorbance around 280 nm and enhanced fluorescence emission with excitation at 285 nm. Fluorescence quenching experiments of the proteins by acrylamide and KI indicate that more surface accessible tryptophan residues are exposed in GMb. CD spectroscopic study reveals a change in the secondary structure of GMb with decreased alpha-helix content. 1-anilino-naphthaline-8-sulfonate (ANS) binding with Mb and GMb indicates that glycation increases hydrophobicity of the heme protein. GMb appears to be less stable with respect to thermal denaturation and differential calorimetry experiments. Heme-globin linkage becomes weaker in GMb, as shown by spectroscopic and gel electrophoresis experiments. A correlation between glycation-induced structural and functional modifications of the heme protein has been suggested.

  14. Complex nanoprecipitate structures induced by irradiation in immiscible alloy systems

    NASA Astrophysics Data System (ADS)

    Shu, Shipeng; Bellon, P.; Averback, R. S.

    2013-04-01

    We investigate the fundamentals of compositional patterning induced by energetic particle irradiation in model A-B substitutional binary alloys using kinetic Monte Carlo simulations. The study focuses on a type of nanostructure that was recently observed in dilute Cu-Fe and Cu-V alloys, where precipitates form within precipitates, a morphology that we term “cherry-pit” structures. The simulations show that the domain of stability of these cherry-pit structures depends on the thermodynamic and kinetic asymmetry between the A and B elements. In particular, both lower solubilities and diffusivities of A in B compared to those of B in A favor the stabilization of these cherry-pit structures for A-rich average compositions. The simulation results are rationalized by extending the analytic model introduced by Frost and Russell for irradiation-induced compositional patterning so as to include the possible formation of pits within precipitates. The simulations indicate also that the pits are dynamical structures that undergo nearly periodic cycles of nucleation, growth, and absorption by the matrix.

  15. Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site

    SciTech Connect

    Yang, Hua; Chen, Li-Mei; Carney, Paul J.; Donis, Ruben O.; Stevens, James

    2012-02-21

    Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  16. Identifying structures in clouds of induced microseismic events

    SciTech Connect

    Fehler, M.; House, L.; Phillips, W.S.

    1997-07-01

    A method for finding improved relative locations of microearthquakes accompanying fluid production and injection is presented. The method is based on the assumption that the microearthquake locations are more clustered than found when events are located using conventional techniques. By allowing the rms misfit between measured arrival times and predicted arrival times to increase if events move closer together, the authors find that there is more structure in the pattern of seismic locations. The method is demonstrated using a dataset of microearthquakes induced by hydraulic fracturing. The authors find that structures found using relative arrival times of events having similar waveforms to find improved relative locations of events can also be recovered using the new inversion method but without the laborious repicking procedure. The method provides improved relative locations and hence, an improved image of the structure within the seismic zone that may allow for a better relation between microearthquake locations and zones of increased fluid permeability to be found.

  17. Wiring of metallized microtubules by electron beam-induced structuring

    NASA Astrophysics Data System (ADS)

    Fritzsche, Wolfgang; Köhler, J. Michael; Böhm, Konrad J.; Unger, Eberhard; Wagner, Thomas; Kirsch, Remo; Mertig, Michael; Pompe, Wolfgang

    1999-09-01

    Molecular electronics emerge as a possibility to continue the miniaturization of electronic circuits down to the lower nanometre scale. One significant challenge is the electrical connection of molecular devices by nanowires. We present here the realization of a new approach for the wiring of nanostructures by linking metallized microtubules (MTs) to prestructured microelectrodes. MTs (tube-like protein structures) were metallized and deposited on microstructured substrates. Electron beam-induced deposition was used for structuring connecting gold lines as nanoelectrodes, which wire a single MT to microelectrodes created by photolithography. Initial electrical measurements confirmed the suitability of the set-up for linking nanometre-scale structures to a measurement device. A metallized MT yielded a resistance below 50 icons/Journals/Common/Omega" ALT="Omega" ALIGN="TOP"/> over the length of 1 µm.

  18. The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C.

    PubMed Central

    Joost Haasnoot, P C; Olsthoorn, René C L; Bol, John F

    2002-01-01

    In the Bromoviridae family of plant viruses, trinucleotide hairpin loops play an important role in RNA transcription. Recently, we reported that Brome mosaic virus (BMV) subgenomic (sg) transcription depended on the formation of an unusual triloop hairpin. By native gel electrophoresis, enzymatic structure probing, and NMR spectroscopy it is shown here that in the absence of viral replicase the hexanucleotide loop 5'C1AUAG5A3' of this RNA structure can adopt a pseudo trinucleotide loop conformation by transloop base pairing between C1 and G5. By means of in vitro replication assays using partially purified BMV RNA-dependent RNA polymerase (RdRp) it was found that other base pairs contribute to sg transcription, probably by stabilizing the formation of this pseudo triloop, which is proposed to be the primary element recognized by the viral replicase. The BMV pseudo triloop structure strongly resembles iron-responsive elements (IREs) in cellular messenger RNAs and may represent a general protein-binding motif. In addition, in vitro replication assays showed that the BMV sg hairpin is functionally equivalent to the minus-strand core promoter hairpin stem-loop C at the 3' end of BMV RNAs. Replacement of the sg hairpin by stem-loop C yielded increased sg promoter activity whereas replacement of stem-loop C by the sg hairpin resulted in reduced minus-strand promoter activity. We conclude that AUA triloops represent the common motif in the BMV sg and minus-strand promoters required for recruitment of the viral replicase. Additional sequence elements of the minus-strand promoter are proposed to direct the RdRp to the initiation site at the 3' end of the genomic RNA. PMID:11873757

  19. Membrane-Docking Loops of the cPLA2 C2 Domain: Detailed Structural Analysis of the Protein-Membrane Interface via Site-Directed Spin-Labeling†

    PubMed Central

    Malmberg, Nathan J.; Van Buskirk, David R.; Falke, Joseph J.

    2013-01-01

    C2 domains are protein modules found in numerous eukaryotic signaling proteins, where their function is to target the protein to cell membranes in response to a Ca2+ signal. Currently, the structure of the interface formed between the protein and the phospholipid bilayer is inaccessible to high-resolution structure determination, but EPR site-directed spin-labeling can provide a detailed medium-resolution view of this interface. To apply this approach to the C2 domain of cytosolic phospholipase A2 (cPLA2), single cysteines were introduced at all 27 positions in the three Ca2+-binding loops and labeled with a methanethiosulfonate spin-label. Altogether, 24 of the 27 spin-labeled domains retained Ca2+-activated phospholipid binding. EPR spectra of these 24 labeled domains obtained in the presence and absence of Ca2+ indicate that Ca2+ binding triggers subtle changes in the dynamics of two localized regions within the Ca2+-binding loops: one face of the loop 1 helix and the junction between loops 1 and 2. However, no significant changes in loop structure were detected upon Ca2+ binding, nor upon Ca2+-triggered docking to membranes. EPR depth parameters measured in the membrane-docked state allow determination of the penetration depth of each residue with respect to the membrane surface. Analysis of these depth parameters, using an improved, generalizable geometric approach, provides the most accurate picture of penetration depth and angular orientation currently available for a membrane-docked peripheral protein. Finally, the observation that Ca2+ binding does not trigger large rearrangements of the membrane-docking loops favors the electrostatic switch model for Ca2+ activation and disfavors, or places strong constraints on, the conformational switch model. PMID:14609334

  20. Structural characteristics correlate with immune responses induced by HIV envelope glycoprotein vaccines.

    PubMed

    Sharma, Victoria A; Kan, Elaine; Sun, Yide; Lian, Ying; Cisto, Jimna; Frasca, Verna; Hilt, Susan; Stamatatos, Leonidas; Donnelly, John J; Ulmer, Jeffrey B; Barnett, Susan W; Srivastava, Indresh K

    2006-08-15

    HIV envelope glycoprotein (Env) is the target for inducing neutralizing antibodies. Env is present on the virus surface as a trimer, and, upon binding to CD4, a cascade of events leads to structural rearrangement exposing the co-receptor binding site and entry into the CD4+ host target cells. We have designed monomeric and trimeric Env constructs with and without deletion of the variable loop 2 (ΔV2) from SF162, a subtype B primary isolate, and performed biophysical, biochemical and immunological studies to establish a potential structure–functional relationship. We expressed these Envs in CHO cells, purified the proteins to homogeneity and performed biophysical studies to define the binding properties to CD4, structural characteristics and exposure of epitopes recognized by b12 and CD4i mAb (17B) on both full-length and mutant HIV Env proteins. Parameters evaluated include oligomerization state, number and affinity of CD4 binding sites, enthalpy and entropy of the Env–CD4 interaction and affinity for b12 and 17b mAbs. We observed one CD4 binding site per monomer and three active CD4 binding sites per trimer. A40-fold difference in affinity of the gp120 monomer vs. the o-gp140 trimer towards CD4 was observed (Kd = 58 nM and 1.5 nM, respectively),whereas only a 2-fold difference was observed for the V2 deleted Envs (Kd of gp120ΔV2 = 19 nM, Kd of o-gp140DV2 = 9.3 nM). Monomers had 3-fold higher affinity to the mAb 17b and at least 3-fold weaker affinity to b12 compared to trimers, with gp120DV2 having the weakest affinity for b12 (Kd = 446 nM). Affinity of CD4 binding correlated with proportion of the antibodies induced against the conformational epitopes by the corresponding Envs, and changes in mAb binding correlated with the induction of antibodies directed against linear epitopes. Furthermore,biophysical analysis reveals that the V2 deletion has broad structural implications in the monomer not shared by the trimer, and these changes are reflected in the

  1. Modulation of activation-loop phosphorylation by JAK inhibitors is binding mode dependent

    PubMed Central

    Bonenfant, Débora; Rubert, Joëlle; Vangrevelinghe, Eric; Scheufler, Clemens; Marque, Fanny; Régnier, Catherine H.; De Pover, Alain; Ryckelynck, Hugues; Bhagwat, Neha; Koppikar, Priya; Goel, Aviva; Wyder, Lorenza; Tavares, Gisele; Baffert, Fabienne; Pissot-Soldermann, Carole; Manley, Paul W.; Gaul, Christoph; Voshol, Hans; Levine, Ross L.; Sellers, William R.; Hofmann, Francesco; Radimerski, Thomas

    2016-01-01

    JAK inhibitors are being developed for the treatment of rheumatoid arthritis, psoriasis, myeloproliferative neoplasms and leukemias. Most of these drugs target the ATP-binding pocket and stabilize the active conformation of the JAK kinases. This type-I binding mode leads to an increase in JAK activation-loop phosphorylation, despite blockade of kinase function. Here we report that stabilizing the inactive state via type-II inhibition acts in the opposite manner, leading to a loss of activation-loop phosphorylation. We used X-ray crystallography to corroborate the binding mode and report for the first time the crystal structure of the JAK2 kinase domain in an inactive conformation. Importantly, JAK inhibitor-induced activation-loop phosphorylation requires receptor interaction, as well as intact kinase and pseudokinase domains. Hence, depending on the respective conformation stabilized by a JAK inhibitor, hyperphosphorylation of the activation-loop may or may not be elicited. PMID:22684457

  2. Telomeres thrown for a loop.

    PubMed

    Haber, James E

    2004-11-19

    A remarkable paper from the de Lange lab (Wang et al., 2004) in a recent issue of Cell reveals that homologous recombination can result in the abrupt shortening of telomeres in a process that appears to involve reciprocal crossing over within the t-loop structure that protects chromosome ends.

  3. Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

    SciTech Connect

    Egli, Martin; Pattanayek, Rekha; Sheehan, Jonathan H.; Xu, Yao; Mori, Tetsuya; Smith, Jarrod A.; Johnson, Carl H.

    2013-01-25

    We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

  4. Spring control of wire harness loops

    NASA Technical Reports Server (NTRS)

    Curcio, P. J.

    1979-01-01

    Negator spring control guides wire harness between movable and fixed structure. It prevents electrical wire harness loop from jamming or being severed as wire moves in response to changes in position of aircraft rudder. Spring-loaded coiled cable controls wire loop regardless of rudder movement.

  5. Induced radioactivity of LDEF materials and structural components

    NASA Technical Reports Server (NTRS)

    Harmon, B. A.; Laird, C. E.; Fishman, G. J.; Parnell, T. A.; Camp, D. C.; Frederick, C. E.; Hurley, D. L.; Lindstrom, D. J.; Moss, C. E.; Reedy, R. C.; Reeves, J. H.; Smith, A. R.; Winn, W. G.; Benton, E. V.

    1996-01-01

    We present an overview of the Long Duration Exposure Facility (LDEF) induced activation measurements. The LDEF, which was gravity-gradient stabilized, was exposed to the low Earth orbit (LEO) radiation environment over a 5.8 year period. Retrieved activation samples and structural components from the spacecraft were analyzed with low and ultra-low background HPGe gamma spectrometry at several national facilities. This allowed a very sensitive measurement of long-lived radionuclides produced by proton- and neutron-induced reactions in the time-dependent, non-isotropic LEO environment. A summary of major findings from this study is given that consists of directionally dependent activation, depth profiles, thermal neutron activation, and surface beryllium-7 deposition from the upper atmosphere. We also describe a database of these measurements that has been prepared for use in testing radiation environmental models and spacecraft design.

  6. Nonlinear effects of a modal domain optical fiber sensor in a vibration suppression control loop for a flexible structure

    SciTech Connect

    Lindner, D.K.; Zvonar, G.A.; Baumann, W.T.; Delos, P.L. . Bradley Dept. of Electrical Engineering)

    1993-01-01

    Recently, a modal domain optical fiber sensor has been demonstrated as a sensor in a control system for vibration suppression of a flexible cantilevered beam. This sensor responds to strain through a mechanical attachment to the structure. Because this sensor is of the interferometric type, the output of the sensor has a sinusoidal nonlinearity. For small levels of strain, the sensor can be operated in its linear region. For large levels of strain, the detection electronics can be configured to count fringes. In both of these configurations, the sensor nonlinearity imposes some restrictions on the performance of the control system. In this paper the authors investigate the effects of these sensor nonlinearities on the control system, and identify the region of linear operation in terms of the optical fiber sensor parameters.

  7. Nonlinear effects of a modal domain optical fiber sensor in a vibration suppression control loop for a flexible structure

    NASA Technical Reports Server (NTRS)

    Lindner, D. K.; Zvonar, G. A.; Baumann, W. T.; Delos, P. L.

    1993-01-01

    Recently, a modal domain optical fiber sensor has been demonstrated as a sensor in a control system for vibration suppression of a flexible cantilevered beam. This sensor responds to strain through a mechanical attachment to the structure. Because this sensor is of the interferometric type, the output of the sensor has a sinusoidal nonlinearity. For small levels of strain, the sensor can be operated in its linear region. For large levels of strain, the detection electronics can be configured to count fringes. In both of these configurations, the sensor nonlinearity imposes some restrictions on the performance of the control system. In this paper we investigate the effects of these sensor nonlinearities on the control system, and identify the region of linear operation in terms of the optical fiber sensor parameters.

  8. Multi-instrument observations of coronal loops

    NASA Astrophysics Data System (ADS)

    Scott, Jason Terrence

    This document exhibits results of analysis from data collected with multiple EUV satellites (SOHO, TRACE, STEREO, Hinode, and SDO). The focus is the detailed observation of coronal loops using multiple instruments, i.e. filter imagers and spectrometers. Techniques for comparing the different instruments and deriving loop parameters are demonstrated. Attention is given to the effects the different instruments may introduce into the data and their interpretation. The assembled loop parameters are compared to basic energy balance equations and scaling laws. Discussion of the blue-shifted, asymmetric, and line broadened spectral line profiles near the footpoints of coronal loops is made. The first quantitative analysis of the anti-correlation between intensity and spectral line broadening for isolated regions along loops and their footpoints is presented. A magnetic model of an active region shows where the separatrices meet the photospheric boundary. At the boundary, the spectral data reveal concentrated regions of increased blue-shifted outflows, blue wing asymmetry, and line broadening. This is found just outside the footpoints of bright loops. The intensity and line broadening in this region are anti-correlated. A comparison of the similarities in the spectroscopic structure near the footpoints of the arcade loops and more isolated loops suggests the notion of consistent structuring for the bright loops forming an apparent edge of an active region core.

  9. Effect of confinement induced structures on suspension rheology

    NASA Astrophysics Data System (ADS)

    Ramaswamy, Meera; Leahy, Brian; Lin, Yen-Chih; Cohen, Itai

    2015-11-01

    Understanding the flow behavior of confined colloidal systems is important in many industrial settings ranging from inkjet printers to pharmaceuticals. Confined colloidal suspensions under shear demonstrate many fascinating responses including vorticity-aligned strings in colloidal liquids and buckled phases in crystals. Despite the extensive studies of these confinement induced structures, the interplay between these exotic structural responses and the suspension rheology remains poorly understood. Here, we use a confocal rheoscope to image the suspension particle configuration while simultaneously measuring its stress responses. The confocal rheoscope has two precisely-aligned parallel plates that can confine the suspension with a variable gap size ranging from 3 to 20 particle diameters, allowing us to measure the response of the system as a function of the gap size. Moreover, we alter the rheological properties of the sample by adding a small amount of dimers. The dimers undergo Jeffery orbits at large strains and deform the confinement induced structures of the spheres, leading to a viscosity change. We discuss the results of these experiments and their implications in the areas of micro and nanofluidics.

  10. Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-β-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus.

    PubMed

    Kim, Min-Kyu; An, Young Jun; Song, Jung Min; Jeong, Chang-Sook; Kang, Mee Hye; Kwon, Kae Kyoung; Lee, Youn-Ho; Cha, Sun-Shin

    2014-11-01

    Endo-β-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus (CaMan), is a cold-adapted β-mannanase that has the lowest optimum temperature (30°C) of all known β-mannanases. Here, we report the apo- and mannopentaose (M5) complex structures of CaMan. Structural comparison of CaMan with other β-mannanases from the multicellular animals reveals that CaMan has an extended loop that alters topography of the active site. Structural and mutational analyses suggest that this extended loop is linked to the cold-adapted enzymatic activity. From the CaMan-M5 complex structure, we defined the mannose-recognition subsites and observed unreported M5 binding site on the surface of CaMan. PMID:25082572

  11. Expression of the Helicobacter pylori virulence factor vacuolating cytotoxin A (vac A) is influenced by a potential stem‐loop structure in the 5′ untranslated region of the transcript

    PubMed Central

    Amilon, Karin R.; Letley, Darren P.; Winter, Jody A.; Robinson, Karen

    2015-01-01

    Summary The vacuolating cytotoxin, VacA, is an important virulence factor secreted by the gastric pathogen H elicobacter pylori. Certain vac A genotypes are strongly associated with disease risk, but the association is not absolute. The factors determining vac A gene expression are not fully understood, and the mechanisms of its regulation are elusive. We have identified a potential mRNA stem‐loop forming structure in the 5′ untranslated region (UTR) of the vac A transcript. Using site‐directed mutagenesis, we found that disruption of the stem‐loop structure reduced steady‐state mRNA levels between two‐ and sixfold (P = 0.0005) and decreased mRNA half‐life compared with wild type (P = 0.03). This led to a marked reduction in VacA protein levels and overall toxin activity. Additionally, during stressful environmental conditions of acid pH or high environmental salt concentrations, when general transcription of vac A was decreased or increased respectively, the stabilising effects of the stem‐loop were even more pronounced. Our results suggest that the stem‐loop structure in the vac A 5′ UTR is an important determinant of vac A expression through stabilisation of the vac A mRNA transcript and that the stabilising effect is of particular importance during conditions of environmental stress. PMID:26259667

  12. Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.

    PubMed

    Guilfoyle, Amy P; Deshpande, Chandrika N; Vincent, Kimberley; Pedroso, Marcelo M; Schenk, Gerhard; Maher, Megan J; Jormakka, Mika

    2014-05-01

    GTPases (G proteins) hydrolyze the conversion of GTP to GDP and free phosphate, comprising an integral part of prokaryotic and eukaryotic signaling, protein biosynthesis and cell division, as well as membrane transport processes. The G protein cycle is brought to a halt after GTP hydrolysis, and requires the release of GDP before a new cycle can be initiated. For eukaryotic heterotrimeric Gαβγ proteins, the interaction with a membrane-bound G protein-coupled receptor catalyzes the release of GDP from the Gα subunit. Structural and functional studies have implicated one of the nucleotide binding sequence motifs, the G5 motif, as playing an integral part in this release mechanism. Indeed, a Gαs G5 mutant (A366S) was shown to have an accelerated GDP release rate, mimicking a G protein-coupled receptor catalyzed release state. In the present study, we investigate the role of the equivalent residue in the G5 motif (residue A143) in the prokaryotic membrane protein FeoB from Streptococcus thermophilus, which includes an N-terminal soluble G protein domain. The structure of this domain has previously been determined in the apo and GDP-bound states and in the presence of a transition state analogue, revealing conformational changes in the G5 motif. The A143 residue was mutated to a serine and analyzed with respect to changes in GTPase activity, nucleotide release rate, GDP affinity and structural alterations. We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base.

  13. Diabetes as a case study of chronic disease management with a personalized approach: the role of a structured feedback loop.

    PubMed

    Ceriello, Antonio; Barkai, László; Christiansen, Jens Sandahl; Czupryniak, Leszek; Gomis, Ramon; Harno, Kari; Kulzer, Bernhard; Ludvigsson, Johnny; Némethyová, Zuzana; Owens, David; Schnell, Oliver; Tankova, Tsvetalina; Taskinen, Marja-Riitta; Vergès, Bruno; Weitgasser, Raimund; Wens, Johan

    2012-10-01

    As non-communicable or chronic diseases are a growing threat to human health and economic growth, political stakeholders are aiming to identify options for improved response to the challenges of prevention and management of non-communicable diseases. This paper is intended to contribute ideas on personalized chronic disease management which are based on experience with one major chronic disease, namely diabetes mellitus. Diabetes provides a pertinent case of chronic disease management with a particular focus on patient self-management. Despite advances in diabetes therapy, many people with diabetes still fail to achieve treatment targets thus remaining at risk of complications. Personalizing the management of diabetes according to the patient's individual profile can help in improving therapy adherence and treatment outcomes. This paper suggests using a six-step cycle for personalized diabetes (self-)management and collaborative use of structured blood glucose data. E-health solutions can be used to improve process efficiencies and allow remote access. Decision support tools and algorithms can help doctors in making therapeutic decisions based on individual patient profiles. Available evidence about the effectiveness of the cycle's constituting elements justifies expectations that the diabetes management cycle as a whole can generate medical and economic benefit.

  14. Structural changes in Tetrahymena rostrata during induced encystment

    SciTech Connect

    McArdle, E.W.; Bergquist, B.L.; Ehret, C.F.

    1980-01-01

    Experimentally induced precystic stages and mature cysts from 3 clones of Tetrahymena rostrata were examined by light and electron microscopy. It was demonstrated by cytochemical staining and fine-structural observations that precystic stages release mucocyst material that provides for the production of a cyst wall. Early and late cysts also contain numerous autophagous vacuoles. In late cysts there is a replacement of depleted mucocyst organelles. The developmental evidence obtained from sampling of sequential developmental stages suggests an approx. 24-h timetable of cytoplasmic events associated with encystment in this organism.

  15. Investigations of pressure induced structural phase transformations in pentaerythritol

    NASA Astrophysics Data System (ADS)

    Garg, Nandini; Sharma, Surinder M.; Sikka, S. K.

    2005-10-01

    We have investigated the pressure induced structural changes in pentaerythritol {2,2-bis-(hydroxymethyl)-1,3-propanediol} with the help of X-ray diffraction studies. Our results show that this compound undergoes transformations to a lower symmetry phase between 5.2-5.9 GPa. It further undergoes phase transformations at ˜8.5 and ˜11 GPa; eventually evolving to a disordered phase beyond 14-15 GPa in agreement with our earlier Raman studies. On release of pressure from 18.5 GPa, the compound transforms back to the initial tetragonal phase.

  16. Light-induced metastable structural changes in hydrogenated amorphous silicon

    SciTech Connect

    Fritzsche, H.

    1996-09-01

    Light-induced defects (LID) in hydrogenated amorphous silicon (a-Si:H) and its alloys limit the ultimate efficiency of solar panels made with these materials. This paper reviews a variety of attempts to find the origin of and to eliminate the processes that give rise to LIDs. These attempts include novel deposition processes and the reduction of impurities. Material improvements achieved over the past decade are associated more with the material`s microstructure than with eliminating LIDs. We conclude that metastable LIDs are a natural by-product of structural changes which are generally associated with non-radiative electron-hole recombination in amorphous semiconductors.

  17. Waves in Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Wang, T. J.

    2016-02-01

    The corona is visible in the optical band only during a total solar eclipse or with a coronagraph. Coronal loops are believed to be plasma-filled closed magnetic flux anchored in the photosphere. Based on the temperature regime, they are generally classified into cool, warm, and hot loops. The magnetized coronal structures support propagation of various types of magnetohydrodynamics (MHD) waves. This chapter reviews the recent progress made in studies based on observations of four types of wave phenomena mainly occurring in coronal loops of active regions, including: flare-excited slow-mode waves; impulsively excited kink-mode waves; propagating slow magnetoacoustic waves; and ubiquitous propagating kink (Alfvénic) waves. This review not only comprehensively discusses these waves and coronal seismology but also topics that are newly emerging or hotly debated in order to provide the reader with useful guidance on further studies.

  18. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    SciTech Connect

    McGuire, S. Miles, R.

    2014-12-28

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}Π{sub g} ← X{sup 1}Σ{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ″1}Σ{sub g}{sup +} electronic state.

  19. Congestion Induced by the Structure of Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Solé-Ribalta, Albert; Gómez, Sergio; Arenas, Alex

    2016-03-01

    Multiplex networks are representations of multilayer interconnected complex networks where the nodes are the same at every layer. They turn out to be good abstractions of the intricate connectivity of multimodal transportation networks, among other types of complex systems. One of the most important critical phenomena arising in such networks is the emergence of congestion in transportation flows. Here, we prove analytically that the structure of multiplex networks can induce congestion for flows that otherwise would be decongested if the individual layers were not interconnected. We provide explicit equations for the onset of congestion and approximations that allow us to compute this onset from individual descriptors of the individual layers. The observed cooperative phenomenon is reminiscent of Braess' paradox in which adding extra capacity to a network when the moving entities selfishly choose their route can in some cases reduce overall performance. Similarly, in the multiplex structure, the efficiency in transportation can unbalance the transportation loads resulting in unexpected congestion.

  20. Irradiation induced structural change in Mo2Zr intermetallic phase

    DOE PAGESBeta

    Gan, J.; Keiser, Jr., D. D.; Miller, B. D.; Eriksson, N.; Sohn, Y. H.; Kirk, M.

    2016-05-14

    The Mo2Zr phase has been identified as a major interaction product at the interface of U-10Mo and Zr. Transmission electron microscopy in-situ irradiation with Kr ions at 200 °C with doses up to 2.0E+16 ions/cm2 was carried out to investigate the radiation stability of the Mo2Zr. The Mo2Zr undergoes a radiation-induced structural change, from a large cubic (cF24) to a small cubic (cI2), along with an estimated 11.2% volume contraction without changing its composition. The structural change begins at irradiation dose below 1.0E+14 ions/cm2. Furthermore, the transformed Mo2Zr phase demonstrates exceptional radiation tolerance with the development of dislocations without bubblemore » formation.« less

  1. Understanding Gas-Induced Structural Deformation of ZIF-8.

    PubMed

    Ania, Conchi O; García-Pérez, E; Haro, M; Gutiérrez-Sevillano, J J; Valdés-Solís, T; Parra, J B; Calero, S

    2012-05-01

    ZIF-8 is a zeolitic imidazolate framework with very good thermal and chemical stability that opens up many applications that are not feasible by other metal-organic frameowrks (MOFs) and zeolites. Several works report the adsorption properties of ZIF-8 for strategic gases. However, despite the vast experimental corpus of data reported, there seems yet to be a dearth in the understanding of the gas adsorption properties. In this work we provide insights at a molecular level on the mechanisms governing the ZIF-8 structural deformation during molecular adsorption. We demonstrate that the ZIF-8 structural deformation during the adsorption of different molecules at cryogenic temperature goes beyond the gas-induced rotation of the imidazolate linkers. We combine experimental and simulation studies to demonstrate that this deformation is governed by the polarizability and molecular size and shape of the gases, and that the stepped adsorption behavior is defined by the packing arrangement of the guest inside the host. PMID:26288051

  2. Field-induced structure of confined ferrofluid emulsion

    SciTech Connect

    Lawrence, E.M.; Ivey, M.L.; Flores, G.A.; Liu, J. . Dept. of Physics and Astronomy); Bibette, J. ); Richard, J. )

    1994-09-01

    Field-induced phase behavior of a confined monodisperse ferrofluid emulsion was studied using optical microscopy, light transmission, and static light scattering techniques. Upon application of magnetic field, randomly-dispersed magnetic emulsion droplets form solid structures at [lambda] = 1.5, where [lambda] is defines as the ratio of the dipole-dipole interaction energy to the thermal energy at room temperature. The new solid phase consists of either single droplet chains, columns, or worm-like clusters, depending on the volume fraction, cell thickness and rate of field application. For the column phase, an equilibrium structure of equally-sized and spaced columns was observed. The measurements taken for cell thickness 5[mu]m [<=] L [<=] 500 [mu]m and volume fraction 0.04 show the column spacing to be reasonably described by d = 1.49 L[sup 0.34].

  3. Chelation-Induced Polymer Structural Hierarchy/Complexity in Water.

    PubMed

    Han, Jie; Zhou, Kaiyi; Zhu, Xuechao; Yu, Qiuping; Ding, Yi; Lu, Xinhua; Cai, Yuanli

    2016-08-01

    Understanding nanoscale structural hierarchy/complexity of hydrophilic flexible polymers is imperative because it can be viewed as an analogue to protein-alike superstructures. However, current understanding is still in infancy. Herein the first demonstration of nanoscale structural hierarchy/complexity via copper chelation-induced self-assembly (CCISA) is presented. Hierarchically-ordered colloidal networks and disks can be achieved by deliberate control of spacer length and solution pH. Dynamic light scattering, transmission electron microscopy, and atomic force microscopy demonstrate that CCISA underwent supramolecular-to-supracolloidal stepwise-growth mechanism, and underline amazing prospects to the hierarchically-ordered superstructures of hydrophilic flexible polymers in water. PMID:27219860

  4. Mirror domain structures induced by interlayer magnetic wall coupling.

    PubMed

    Lew, W S; Li, S P; Lopez-Diaz, L; Hatton, D C; Bland, J A C

    2003-05-30

    We have found that during giant magnetoresistance measurements in approximately 10 x 10 mm(2) NiFe/Cu/Co continuous film spin-valve structures, the resistance value suddenly drops to its absolute minimum during the NiFe reversal. The results reveal that the alignment of all magnetic domains in the NiFe film follow exactly that of corresponding domains in the Co film for an appropriate applied field strength. This phenomenon is caused by trapping of the NiFe domain walls through the magnetostatic interaction with the Co domain-wall stray fields. Consequently, the interlayer domain-wall coupling induces a mirror domain structure in the magnetic trilayer. PMID:12786582

  5. EVIDENCE OF SOLAR FLARE TRIGGERING DUE TO LOOP-LOOP INTERACTION CAUSED BY FOOTPOINT SHEAR MOTION

    SciTech Connect

    Kumar, Pankaj; Srivastava, A. K.; Uddin, Wahab; Somov, B. V.; Manoharan, P. K.; Erdelyi, R. E-mail: aks@aries.res.i

    2010-11-10

    We analyze multi-wavelength data of an M7.9/1N class solar flare which occurred on 2006 April 27 in AR NOAA 10875. GOES soft X-ray images provide the most likely signature of two interacting loops and their reconnection, which triggers the solar flare. TRACE 195 A images also reveal the loop-loop interaction and the formation of 'X' points with converging motion ({approx}30 km s{sup -1}) at the reconnection site in between this interacting loop system. This provides evidence of progressive reconnection and flare maximization at the interaction site in the active region. The absence of type III radio bursts during this time period indicates no opening of magnetic field lines during the flare energy release, which implies that the change of field line connectivity/orientation occurred only during the loop-loop interaction and reconnection process. The Ondrejov dynamic radio spectrum shows an intense decimetric (DCIM) radio burst (2.5-4.5 GHz, duration {approx}3 minutes) during the flare initiation, which reveals the signature of particle acceleration from the reconnection site during loop-loop interaction. The double-peak structures at 4.9 and 8.8 GHz provide the most likely confirmatory signature of the loop-loop interaction at the flare site in the active region. RHESSI hard X-ray images also show the loop-top and footpoint sources of the corresponding two-loop system, which act like current-carrying flux tubes with resultant opposite magnetic fields and net force of attraction, and their coalescence during the flare maximum. We also suggest that the shear motion/rotation of the footpoint of the smaller loop, which is anchored in the opposite polarity spot, may be responsible for the flare energy buildup and its eventual release due to the loop-loop interaction.

  6. Mutational analysis of three predicted 5'-proximal stem-loop structures in the genome of tick-borne encephalitis virus indicates different roles in RNA replication and translation

    SciTech Connect

    Rouha, Harald; Hoenninger, Verena M.; Thurner, Caroline; Mandl, Christian W.

    2011-08-15

    Flavivirus gene expression is modulated by RNA secondary structure elements at the terminal ends of the viral RNA molecule. For tick-borne encephalitis virus (TBEV), four stem-loop (SL) elements have been predicted in the first 180 nucleotides of the viral genome: 5'-SL1, 5'-SL2, 5'-SL3 and 5'-SL4. The last three of these appear to be unique to tick-borne flaviviruses. Here, we report their characterization by mutagenesis in a TBEV luciferase reporter system. By manipulating their thermodynamic properties, we found that an optimal stability of the 5'-SL2 is required for efficient RNA replication. 5'-SL3 formation is also important for viral RNA replication, but although it contains the viral start codon, its formation is dispensable for RNA translation. 5'-SL4 appears to facilitate both RNA translation and replication. Our data suggest that maintenance of the balanced thermodynamic stability of these SL elements is important for temporal regulation of its different functions.

  7. Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region.

    PubMed

    Menezes, M R; Kumar, G; Kunal, S P

    2012-05-01

    Genetic structure of skipjack tuna Katsuwonus pelamis from the Indian region was investigated using sequence data of mitochondrial DNA (mtDNA) D-loop region. A total of 315 individuals were sampled from six major fishing grounds around the east and west coasts of India including the Andaman (Port Blair) and Lakshadweep (Minicoy) Islands. Nucleotide and gene diversities were high in all the sample collections. Significant genetic heterogeneity was observed for the mtDNA sequence data among sites (φ(ST) = 0·0273, P < 0·001). Analysis of molecular variance (AMOVA) showed significant genetic variation among four groups (φ(CT) = 0·0261, P < 0·05) which was also supported by spatial AMOVA results. The null hypothesis of single panmictic population of K. pelamis along the Indian coast can thus be rejected. Phylogenetic analysis of the mtDNA sequence data showed the presence of four clades of K. pelamis in the Indian waters. There was no clear pattern, however, of haplotypes and geographic location among samples. The results of this study suggest the occurrence of four genetically differentiated groups of K. pelamis across the coastal waters of India.

  8. Characterization of flow-induced structures in carbon nanotube suspensions

    NASA Astrophysics Data System (ADS)

    Khalkhal, Fatemeh

    Carbon nanotubes (CNTs) are fibre-like nano-particles with many different applications. Due to their high specific surface area, high electric current density, thermal stability and excellent mechanical properties, they are used to reinforce physical properties of polymer matrices. The macroscopic properties of suspensions are inherited from their properties at micron and sub-micron scales. The suspensions structure can be easily influenced by many parameters such as the extent of external shear forces, the suspension concentration, temperature, the particles specifications, etc. This makes the study of the suspension structure a very challenging task and has been the subject of interest to many researchers. In this thesis, the structure of a model carbon nanotube suspension dispersed in an epoxy is studied by employing a set of rheological methods, scaling and fractal theories and a structural thixotropic model. The effect of flow history on linear viscoelastic properties of suspensions and the evolution of structure upon cessation of shear flow has been studied over a wide range of pre-shearing rates, concentration and temperature. The results of these analyses are as follows. The effect of flow history is more pronounced on the suspensions structure in dilute and semi-dilute concentration regimes. By pre-shearing at low rates, more inter-particle entanglements were induced, which resulted in reduction of rheological percolation thresholds. After cessation of shear flow, for dilute and semi-dilute suspensions, the formed metastable structures were distinguishable by different storage moduli, which were inversely related to the rate of pre-shearing. However, for the concentrated suspensions, the formed metastable structures had an approximately equal storage modulus regardless of the rate of the applied pre-shearing. It was shown that the rate of formation of these metastable structures was enhanced by increasing concentration. Furthermore, the rate of structure

  9. Mechanically Induced Intercellular Calcium Communication in Confined Endothelial Structures

    PubMed Central

    Junkin, Michael; Lu, Yi; Long, Juexuan; Deymier, Pierre A.; Hoying, James B.; Wong, Pak Kin

    2012-01-01

    Calcium signaling in the diverse vascular structures is regulated by a wide range of mechanical and biochemical factors to maintain essential physiological functions of the vasculature. To properly transmit information, the intercellular calcium communication mechanism must be robust against various conditions in the cellular microenvironment. Using plasma lithography geometric confinement, we investigate mechanically induced calcium wave propagation in networks of human umbilical vein endothelial cells organized. Endothelial cell networks with confined architectures were stimulated at the single cell level, including using capacitive force probes. Calcium wave propagation in the network was observed using fluorescence calcium imaging. We show that mechanically induced calcium signaling in the endothelial networks is dynamically regulated against a wide range of probing forces and repeated stimulations. The calcium wave is able to propagate consistently in various dimensions from monolayers to individual cell chains, and in different topologies from linear patterns to cell junctions. Our results reveal that calcium signaling provides a robust mechanism for cell-cell communication in networks of endothelial cells despite the diversity of the microenvironmental inputs and complexity of vascular structures. PMID:23267827

  10. Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 (HIV-1) V3 Loop Chimeras from a Combinatorial Library Induce Potent Neutralizing Antibody Responses against HIV-1

    PubMed Central

    Smith, Allen D.; Geisler, Sheila C.; Chen, Anne A.; Resnick, Dawn A.; Roy, Birgit M.; Lewi, Paul J.; Arnold, Edward; Arnold, Gail Ferstandig

    1998-01-01

    In an effort to develop a useful AIDS vaccine or vaccine component, we have generated a combinatorial library of chimeric viruses in which the sequence IGPGRAFYTTKN from the V3 loop of the MN strain of human immunodeficiency virus type 1 (HIV-1) is displayed in many conformations on the surface of human rhinovirus 14 (HRV14). The V3 loop sequence was inserted into a naturally immunogenic site of the cold-causing HRV14, bridged by linkers consisting of zero to three randomized amino acids on each side. The library of chimeric viruses obtained was subjected to a variety of immunoselection schemes to isolate viruses that provided the most useful presentations of the V3 loop sequence for potential use in a vaccine against HIV. The utility of the presentations was assessed by measures of antigenicity and immunogenicity. Most of the immunoselected chimeras examined were potently neutralized by each of the four different monoclonal anti-V3 loop antibodies tested. Seven of eight chimeric viruses were able to elicit neutralizing antibody responses in guinea pigs against the MN and ALA-1 strains of HIV-1. Three of the chimeras elicited HIV neutralization titers that exceeded those of all but a small number of previously described HIV immunogens. These results indicate that HRV14:HIV-1 chimeras may serve as useful immunogens for stimulating immunity against HIV-1. This method can be used to flexibly reconstruct varied immunogens on the surface of a safe and immunogenic vaccine vehicle. PMID:9420270

  11. Double hysteresis loop induced by defect dipoles in ferroelectric Pb(Zr{sub 0.8}Ti{sub 0.2})O{sub 3} thin films

    SciTech Connect

    Pu Yunti; Zhu Jiliang; Zhu Xiaohong; Luo Yuansheng; Wang Mingsong; Li Xuhai; Liu Jing; Zhu Jianguo; Xiao Dingquan

    2011-02-15

    Pb(Zr{sub 0.8}Ti{sub 0.2})O{sub 3} (PZT80/20) thin films were deposited on the Pt(111)/Ti/SiO{sub 2}/Si(100) substrates by RF magnetron sputtering. Mainly perovskite crystalline phase with highly (202)-preferred orientation, determined by x-ray diffraction, was formed in the lead zirconate titanate (PZT)(80/20) thin films. Polarization measurements of the unannealed and aged films showed a clear double hysteresis loop. However, the double hysteresis loop phenomenon was greatly suppressed in the PZT thin films annealed under pure oxygen, and thus they exhibited larger remnant polarization (P{sub r} = 6.3 {mu}C/cm{sup 2}). The related mechanism for the appearance of constricted and double hysteresis loops was investigated to be associated with the realignment and disassociation of defect dipoles via oxygen octahedral rotations or oxygen vacancy diffusion. The butterfly-shaped C-V characteristic curve with a valley gave further evidence for double hysteresis loop characteristic in the unannealed and aged PZT thin films.

  12. Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.

    PubMed

    Julien, Jean-Philippe; Bryson, Steve; Nieva, Jose L; Pai, Emil F

    2008-12-12

    2F5 is a monoclonal antibody with potent and broadly neutralizing activity against HIV-1. It targets the membrane-proximal external region (MPER) of the gp41 subunit of the envelope glycoprotein and interferes with the process of fusion between viral and host cell membranes. This study presents eight 2F5 F(ab)' crystal structures in complex with various gp41 peptide epitopes. These structures reveal several key features of this antibody-antigen interaction. (1) Whenever free of contacts caused by crystal artifacts, the extended complementarity-determining region H3 loop is mobile; this is true for ligand-free and epitope-bound forms. (2) The interaction between the antibody and the gp41 ELDKWA epitope core is absolutely critical, and there are also close and specific contacts with residues located N-terminal to the epitope core. (3) Residues located at the C-terminus of the gp41 ELDKWA core do not interact as tightly with the antibody. However, in the presence of a larger peptide containing the gp41 fusion peptide segment, these residues adopt a conformation consistent with the start of an alpha-helix. (4) At high sulfate concentrations, the electron density maps of 2F5 F(ab)'-peptide complexes contain a peak that may mark a binding site for phosphate groups of negatively charged lipid headgroups. The refined atomic-level details of 2F5 paratope-epitope interactions revealed here should contribute to a better understanding of the mechanism of 2F5-based virus neutralization, in general, and prove important for the design of potential vaccine candidates intended to elicit 2F5-like antibody production.

  13. TonB induces conformational changes in surface-exposed loops of FhuA, outer membrane receptor of Escherichia coli

    PubMed Central

    James, Karron J.; Hancock, Mark A.; Moreau, Violaine; Molina, Franck; Coulton, James W.

    2008-01-01

    FhuA, outer membrane receptor of Escherichia coli, transports hydroxamate-type siderophores into the periplasm. Cytoplasmic membrane–anchored TonB transduces energy to FhuA to facilitate siderophore transport. Because the N-terminal cork domain of FhuA occludes the C-terminal β-barrel lumen, conformational changes must occur to enable siderophore passage. To localize conformational changes at an early stage of the siderophore transport cycle, four anti-FhuA monoclonal antibodies (mAbs) were purified to homogeneity, and the epitopes that they recognize were determined by phage display. We mapped continuous and discontinuous epitopes to outer surface-exposed loops 3, 4, and 5 and to β-barrel strand 14. To probe for conformational changes of FhuA, surface plasmon resonance measured mAb binding to FhuA in its apo- and siderophore-bound states. Changes in binding kinetics were observed for mAbs whose epitopes were mapped to outer surface-exposed loops. Further, we measured mAb binding in the absence and presence of TonB. After forming immobilized FhuA–TonB complexes, changes in kinetics of mAb binding to FhuA were even more pronounced compared with kinetics of binding in the absence of TonB. Measurement of extrinsic fluorescence of the dye MDCC conjugated to residue 336 in outer surface-exposed loop 4 revealed 33% fluorescence quenching upon ferricrocin binding and up to 56% quenching upon TonB binding. Binding of mAbs to apo- and ferricrocin-bound FhuA complemented by fluorescence spectroscopy studies showed that their cognate epitopes on loops 3, 4, and 5 undergo conformational changes upon siderophore binding. Further, our data demonstrate that TonB binding promotes conformational changes in outer surface-exposed loops of FhuA. PMID:18653801

  14. Drosophila melanogaster kl-3 and kl-5 Y-loops harbor triple-stranded nucleic acids.

    PubMed

    Piergentili, Roberto; Mencarelli, Caterina

    2008-05-15

    Primary spermatocyte nuclei of Drosophila melanogaster contain three prominent lampbrush-like loops. The development of these structures has been associated with the transcription of three fertility factors located on the Y chromosome, named kl-5, kl-3 and ks-1. These loci have huge physical dimensions and contain extremely long introns. In addition, kl-3 and kl-5 were shown to encode two putative dynein subunits required for the correct assembly of the sperm axoneme. Here, we show that both the kl-5 and kl-3 loops are intensely decorated by monoclonal antibodies recognizing triple-stranded nucleic acids, and that each loop presents a peculiar molecular organization of triplex structures. Moreover, immunostaining of Drosophila hydei primary spermatocytes revealed that also in this species - which diverged from D. melanogaster 58 million years ago - Y-loops are decorated by anti-triplex antibodies, strongly suggesting a conserved role of loop-associated triplexes. Finally, we showed that in D. melanogaster wild-type lines that are raised at the non-permissive temperature of 31+/-0.5 degrees C (which is known to induce male sterility in flies) both the triplex immunostaining and the axonemal dynein heavy chains encoded by kl-3 and kl-5 are no longer detectable, which suggests a functional correlation between loop-associated triplexes, the presence of axonemal proteins and male fertility in fly.

  15. Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop?

    PubMed

    Guerra, Yasel; Valiente, Pedro A; Pons, Tirso; Berry, Colin; Rudiño-Piñera, Enrique

    2016-08-01

    Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop.

  16. Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop?

    PubMed

    Guerra, Yasel; Valiente, Pedro A; Pons, Tirso; Berry, Colin; Rudiño-Piñera, Enrique

    2016-08-01

    Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop. PMID:27329566

  17. Comparison of viscoelastic, structural, and material properties of double-looped anterior cruciate ligament grafts made from bovine digital extensor and human hamstring tendons.

    PubMed

    Donahue, T L; Gregersen, C; Hull, M L; Howell, S M

    2001-04-01

    Due to ready availability, decreased cost, and freedom from transmissible diseases in humans such as hepatitis and AIDS, it would be advantageous to use tendon grafts from farm animals as a substitute for human tendon grafts in in vitro experiments aimed at improving the outcome of anterior cruciate ligament (ACL) reconstructive surgery. Thus the objective of this study was to determine whether an anterior cruciate ligament (ACL) graft composed of two loops of bovine common digital extensor tendon has the same viscoelastic, structural, and material properties as a graft composed of a double loop of semitendinosus and gracilis tendons from humans. To satisfy this objective, grafts were constructed from each tissue source. The cross-sectional area was measured using an area micrometer, and each graft was then pulled using a materials testing system while submerged in a saline bath. Using two groups of tendon grafts (n = 10), viscoelastic tests were conducted over a three-day period during which a constant displacement load relaxation test was followed by a constant amplitude, cyclic load creep test (first day), a constant load creep test (second day), and an incremental cyclic load creep test (third day). Load-to-failure tests were performed on two different groups of grafts (n = 8). When the viscoelastic behavior was compared, there were no significant differences in the rate of load decay or the final load (relaxation test) and rates of displacement increase or final displacements (creep tests) (p > 0.115). To compare both the structural and material properties in the toe region (i.e., < 250 N) of the load-elongation curve, the tangent stiffness and modulus functions were computed from parameters used in an exponential model fit to the load (stress)-elongation (strain) data. Although one of the two parameters in the functions was different statistically, this difference translated into a difference of only 0.03 mm in displacement at 250 N of load. In the linear

  18. The 21 cm signature of a cosmic string loop

    SciTech Connect

    Pagano, Michael; Brandenberger, Robert E-mail: rhb@physics.mcgill.ca

    2012-05-01

    Cosmic string loops lead to nonlinear baryon overdensities at early times, even before the time which in the standard LCDM model corresponds to the time of reionization. These overdense structures lead to signals in 21 cm redshift surveys at large redshifts. In this paper, we calculate the amplitude and shape of the string loop-induced 21 cm brightness temperature. We find that a string loop leads to a roughly elliptical region in redshift space with extra 21 cm emission. The excess brightness temperature for strings with a tension close to the current upper bound can be as high as 1deg K for string loops generated at early cosmological times (times comparable to the time of equal matter and radiation) and observed at a redshift of z+1 = 30. The angular extent of these predicted 'bright spots' is x{sup '}. These signals should be detectable in upcoming high redshift 21 cm surveys. We also discuss the application of our results to global monopoles and primordial black holes.

  19. Helicoids, wrinkles, and loops in twisted ribbons.

    PubMed

    Chopin, Julien; Kudrolli, Arshad

    2013-10-25

    We investigate the instabilities of a flat elastic ribbon subject to twist under tension and develop an integrated phase diagram of the observed shapes and transitions. We find that the primary buckling mode switches from being localized longitudinally along the length of the ribbon to transverse above a triple point characterized by a crossover tension that scales with ribbon elasticity and aspect ratio. Far from threshold, the longitudinally buckled ribbon evolves continuously into a self-creased helicoid with focusing of the curvature along the triangular edges. Further twist causes an anomalous transition to loops compared with rods due to the self-rigidity induced by the creases. When the ribbon is twisted under high tension, transverse wrinkles are observed due to the development of compressive stresses with higher harmonics for greater width-to-length ratios. Our results can be used to develop functional structures using a wide range of elastic materials and length scales.

  20. DISSECTING STRUCTURAL AND ELECTRONIC EFFECTS IN INDUCIBLE NITRIC OXIDE SYNTHASE

    PubMed Central

    Hannibal, Luciana; Page, Richard C.; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J.

    2015-01-01

    Nitric oxide synthases (NOS) are haem-thiolate enzymes that catalyse the conversion of L-Arginine (LArg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide an H-bond for oxygen activation (O-O scission). We present a comparative study of native iNOS versus iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to their native counterparts. Single turnover reactions catalysed by iNOSoxy with LArg (first reaction step) or N-hydroxyarginine (second reaction step) showed that mesohaem substitution triggered faster rates of FeIIO2 conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared to the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency toward NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations. PMID:25608846

  1. Dissecting structural and electronic effects in inducible nitric oxide synthase.

    PubMed

    Hannibal, Luciana; Page, Richard C; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J

    2015-04-01

    Nitric oxide synthases (NOSs) are haem-thiolate enzymes that catalyse the conversion of L-arginine (L-Arg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide a hydrogen bond for oxygen activation (O-O scission). We present a study of native iNOS compared with iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to those of their native counterparts. Single turnover reactions catalysed by iNOSoxy with L-Arg (first reaction step) or N-hydroxy-L-arginine (second reaction step) showed that mesohaem substitution triggered higher rates of Fe(II)O₂ conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared with the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency towards NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations.

  2. Sulfur-induced structural motifs on copper and gold surfaces

    NASA Astrophysics Data System (ADS)

    Walen, Holly

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. We choose very specific conditions: very low temperature (5 K), and very low sulfur coverage (≤ 0.1 monolayer). In this region of temperature-coverage space, which has not been examined previously for these adsorbate-metal systems, the effects of individual interactions between metals and sulfur are most apparent and can be assessed extensively with the aid of theory and modeling. Furthermore, at this temperature diffusion is minimal and relatively-mobile species can be isolated, and at low coverage the structures observed are not consumed by an extended reconstruction. The primary experimental technique is scanning tunneling microscopy (STM). The experimental observations presented here---made under identical conditions---together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  3. Platinum-induced structural collapse in layered oxide polycrystalline films

    SciTech Connect

    Wang, Jianlin; Liu, Changhui; Huang, Haoliang; Fu, Zhengping; Peng, Ranran E-mail: yllu@ustc.edu.cn; Zhai, Xiaofang; Lu, Yalin E-mail: yllu@ustc.edu.cn

    2015-03-30

    Effect of a platinum bottom electrode on the SrBi{sub 5}Fe{sub 1−x}Co{sub x}Ti{sub 4}O{sub 18} layered oxide polycrystalline films was systematically studied. The doped cobalt ions react with the platinum to form a secondary phase of PtCoO{sub 2}, which has a typical Delafossite structure with a weak antiferromagnetism and an exceptionally high in-plane electrical conductivity. Formation of PtCoO{sub 2} at the interface partially consumes the cobalt dopant and leads to the structural collapsing from 5 to 4 layers, which was confirmed by X-ray diffraction and high resolution transmission electron microscopy measurements. Considering the weak magnetic contribution from PtCoO{sub 2}, the observed ferromagnetism should be intrinsic of the Aurivillius compounds. Ferroelectric properties were also indicated by the piezoresponse force microscopy. In this work, the platinum induced secondary phase at the interface was observed, which has a strong impact on Aurivillius structural configuration and thus the ferromagnetic and ferroelectric properties.

  4. G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments

    PubMed Central

    Ivanov, Pavel; O’Day, Elizabeth; Emara, Mohamed M.; Wagner, Gerhard; Lieberman, Judy; Anderson, Paul

    2014-01-01

    Angiogenin (ANG) is a stress-activated ribonuclease that promotes the survival of motor neurons. Ribonuclease inactivating point mutations are found in a subset of patients with ALS, a fatal neurodegenerative disease with no cure. We recently showed that ANG cleaves tRNA within anticodon loops to produce 5′- and 3′-fragments known as tRNA-derived, stress-induced RNAs (tiRNAs). Selected 5′-tiRNAs (e.g., tiRNAAla, tiRNACys) cooperate with the translational repressor Y-box binding protein 1 (YB-1) to displace the cap-binding complex eIF4F from capped mRNA, inhibit translation initiation, and induce the assembly of stress granules (SGs). Here, we show that translationally active tiRNAs assemble unique G-quadruplex (G4) structures that are required for translation inhibition. We show that tiRNAAla binds the cold shock domain of YB-1 to activate these translational reprogramming events. We discovered that 5′-tiDNAAla (the DNA equivalent of 5′-tiRNAAla) is a stable tiRNA analog that displaces eIF4F from capped mRNA, inhibits translation initiation, and induces the assembly of SGs. The 5′-tiDNAAla also assembles a G4 structure that allows it to enter motor neurons spontaneously and trigger a neuroprotective response in a YB-1–dependent manner. Remarkably, the ability of 5′-tiRNAAla to induce SG assembly is inhibited by G4 structures formed by pathological GGGGCC repeats found in C9ORF72, the most common genetic cause of ALS, suggesting that functional interactions between G4 RNAs may contribute to neurodegenerative disease. PMID:25404306

  5. Cyclic universe from Loop Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Cianfrani, Francesco; Kowalski-Glikman, Jerzy; Rosati, Giacomo

    2016-02-01

    We discuss how a cyclic model for the flat universe can be constructively derived from Loop Quantum Gravity. This model has a lower bounce, at small values of the scale factor, which shares many similarities with that of Loop Quantum Cosmology. We find that Quantum Gravity corrections can be also relevant at energy densities much smaller than the Planckian one and that they can induce an upper bounce at large values of the scale factor.

  6. Run-time parallelization and scheduling of loops

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

    1991-01-01

    Run-time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run-time, wavefronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing, and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run-time reordering of loop indexes can have a significant impact on performance.

  7. The structure of truncated recombinant human bile salt-stimulated lipase reveals bile salt-independent conformational flexibility at the active-site loop and provides insights into heparin binding.

    PubMed

    Moore, S A; Kingston, R L; Loomes, K M; Hernell, O; Bläckberg, L; Baker, H M; Baker, E N

    2001-09-21

    Human bile salt-stimulated lipase (BSSL), which is secreted from the pancreas into the digestive tract and from the lactating mammary gland into human milk, is important for the effective absorption of dietary lipids. The dependence of BSSL on bile acids for activity with water-insoluble substrates differentiates it from other lipases. We have determined the crystal structure of a truncated variant of human BSSL (residues 1-5.8) and refined it at 2.60 A resolution, to an R-factor of 0.238 and R(free) of 0.275. This variant lacks the C-terminal alpha-helix and tandem C-terminal repeat region of native BSSL, but retains full catalytic activity. A short loop (residues 115-126) capable of occluding the active-site (the active site loop) is highly mobile and exists in two conformations, the most predominant of which leaves the active-site open for interactions with substrate. The bile salt analogue 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonic acid (CHAPS) was present in the crystallisation medium, but was not observed bound to the enzyme. However, the structure reveals a sulfonate group from the buffer piperizine ethane sulfonic acid (PIPES), making interactions with Arg63 and His115. His115 is part of the active-site loop, indicating that the loop could participate in the binding of a sulphate group from either the glycosaminoglycan heparin (known to bind BSSL) or a bile acid such as deoxycholate. Opening of the 115-126 active-site loop may be cooperatively linked to a sulphate anion binding at this site. The helix bundle domain of BSSL (residues 319-398) exhibits weak electron density and high temperature factors, indicating considerable structural mobility. This domain contains an unusual Asp:Glu pair buried in a hydrophobic pocket between helices alpha(H) and alpha(K) that may be functionally important. We have also solved the structure of full-length glycosylated human BSSL at 4.1 A resolution, using the refined coordinates of the truncated molecule as

  8. Structural alterations of erythrocyte membrane components induced by exhaustive exercise.

    PubMed

    Brzeszczynska, Joanna; Pieniazek, Anna; Gwozdzinski, Lukasz; Gwozdzinski, Krzysztof; Jegier, Anna

    2008-12-01

    Physical exercise was used as a model of the physiological modulator of free radical production to examine the effects of exercise-induced oxidative modifications on the physico-biochemical properties of erythrocyte membrane. The aim of our work was to investigate conformational changes of erythrocyte membrane proteins, membrane fluidity, and membrane susceptibility to disintegration. Venous blood was taken before, immediately after, and 1 h after an exhaustive incremental cycling test (30 W.min-1 ramp), performed by 11 healthy untrained males on balanced diets (mean age, 22 +/- 2 years; mean body mass index, 25 +/- 4.5 kg.m-2). In response to this exercise, individual maximum heart rate was 195 +/- 12 beats.min-1 and maximum wattage was 292 +/- 27 W. Electron paramagnetic resonance spectroscopy was used to investigate alterations in membrane proteins and membrane dynamics, and to measure production of radical species. The reducing potential of plasma (RPP) was measured using the reduction of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and the ferric-reducing ability of plasma. Exercise induced decreases in erythrocyte membrane fluidity in the polar region (p < 0.0001) and alterations in the conformational state of membrane proteins (p < 0.05). An increase in RPP was observed immediately after exercise (p < 0.001), with a further increase 1 h postexercise (p < 0.0001). Supporting measurements of lipid peroxidation showed an increase in thiobarbituric acid reactive substances immediately after exercise (p < 0.05) and at 1 h of recovery (p < 0.001); however, free radicals were not detected. Results indicate the existence of early postexercise mild oxidative stress after single-exercise performance, which induced structural changes in erythrocyte membrane components (protein aggregation) and in the membrane organization (lipids rigidization) that followed lipid peroxidation but did not lead to cellular hemolysis.

  9. Interfacial patterns in magnetorheological fluids: Azimuthal field-induced structures

    NASA Astrophysics Data System (ADS)

    Dias, Eduardo O.; Lira, Sérgio A.; Miranda, José A.

    2015-08-01

    Despite their practical and academic relevance, studies of interfacial pattern formation in confined magnetorheological (MR) fluids have been largely overlooked in the literature. In this work, we present a contribution to this soft matter research topic and investigate the emergence of interfacial instabilities when an inviscid, initially circular bubble of a Newtonian fluid is surrounded by a MR fluid in a Hele-Shaw cell apparatus. An externally applied, in-plane azimuthal magnetic field produced by a current-carrying wire induces interfacial disturbances at the two-fluid interface, and pattern-forming structures arise. Linear stability analysis, weakly nonlinear theory, and a vortex sheet approach are used to access early linear and intermediate nonlinear time regimes, as well as to determine stationary interfacial shapes at fully nonlinear stages.

  10. Interfacial patterns in magnetorheological fluids: Azimuthal field-induced structures.

    PubMed

    Dias, Eduardo O; Lira, Sérgio A; Miranda, José A

    2015-08-01

    Despite their practical and academic relevance, studies of interfacial pattern formation in confined magnetorheological (MR) fluids have been largely overlooked in the literature. In this work, we present a contribution to this soft matter research topic and investigate the emergence of interfacial instabilities when an inviscid, initially circular bubble of a Newtonian fluid is surrounded by a MR fluid in a Hele-Shaw cell apparatus. An externally applied, in-plane azimuthal magnetic field produced by a current-carrying wire induces interfacial disturbances at the two-fluid interface, and pattern-forming structures arise. Linear stability analysis, weakly nonlinear theory, and a vortex sheet approach are used to access early linear and intermediate nonlinear time regimes, as well as to determine stationary interfacial shapes at fully nonlinear stages. PMID:26382499

  11. Endotoxin-Induced Structural Transformations in Liquid Crystalline Droplets

    NASA Astrophysics Data System (ADS)

    Lin, I.-Hsin; Miller, Daniel S.; Bertics, Paul J.; Murphy, Christopher J.; de Pablo, Juan J.; Abbott, Nicholas L.

    2011-06-01

    The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10-5 Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.

  12. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    SciTech Connect

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420{degrees}C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs.

  13. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    SciTech Connect

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420[degrees]C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs.

  14. A PI3K p110β–Rac signalling loop mediates Pten-loss-induced perturbation of haematopoiesis and leukaemogenesis

    PubMed Central

    Yuzugullu, Haluk; Baitsch, Lukas; Von, Thanh; Steiner, Allison; Tong, Haoxuan; Ni, Jing; Clayton, Linda K.; Bronson, Roderick; Roberts, Thomas M.; Gritsman, Kira; Zhao, Jean J.

    2015-01-01

    The tumour suppressor PTEN, which antagonizes PI3K signalling, is frequently inactivated in haematologic malignancies. In mice, deletion of PTEN in haematopoietic stem cells (HSCs) causes perturbed haematopoiesis, myeloproliferative neoplasia (MPN) and leukaemia. Although the roles of the PI3K isoforms have been studied in PTEN-deficient tumours, their individual roles in PTEN-deficient HSCs are unknown. Here we show that when we delete PTEN in HSCs using the Mx1–Cre system, p110β ablation prevents MPN, improves HSC function and suppresses leukaemia initiation. Pharmacologic inhibition of p110β in PTEN-deficient mice recapitulates these genetic findings, but suggests involvement of both Akt-dependent and -independent pathways. Further investigation reveals that a p110β–Rac signalling loop plays a critical role in PTEN-deficient HSCs. Together, these data suggest that myeloid neoplasia driven by PTEN loss is dependent on p110β via p110β–Rac-positive-feedback loop, and that disruption of this loop may offer a new and effective therapeutic strategy for PTEN-deficient leukaemia. PMID:26442967

  15. Structure-induced spin reorientation in magnetic nanostructures

    NASA Astrophysics Data System (ADS)

    Neumann, Alexander; Frauen, Axel; Vollmers, Julian; Meyer, Andreas; Oepen, Hans Peter

    2016-09-01

    We report on structuring-induced changes of the magnetic anisotropy of cylindrical nanostructures which are carved out of thin Pt/Co/Pt films. The magnetic properties of films and structures with a diameter of about 34 nm were investigated via magneto-optic Kerr effect. The magnetic anisotropy is determined for both films and nanostructures for varying Co thicknesses (0.5-7 nm). In general, the nanostructures exhibit larger perpendicular anisotropy than the films. On thickness increase of the Co layer two spin reorientation transitions at about 2.2 and 5 nm are found. At 2.2 nm the nanostructures exhibit the transition from perpendicular to in-plane orientation of magnetization while at 5 nm the reversed transition is found. The variation of the magnetic anisotropy of the Co nanostructures is not solely caused by the change of shape anisotropy. The net change, corrected for the shape, reveals a reduction of strain in the thinnest Co layers while the increase of the anisotropy of the nanostructures at higher Co thicknesses is caused by a transformation of the Co lattice from fcc to hcp.

  16. Mancozeb-induced behavioral deficits precede structural neural degeneration.

    PubMed

    Harrison Brody, A; Chou, Eunice; Gray, Janet M; Pokyrwka, Nancy J; Raley-Susman, Kathleen M

    2013-01-01

    Manganese-containing fungicides like Mancozeb have been associated with neurodegenerative conditions like Parkinson's disease. We examined the behavioral damage and differential neuronal vulnerability resulting from Mancozeb exposure using Caenorhabditis elegans, an important mid-trophic level soil organism that is also a powerful model for studying mechanisms of environmental pollutant-induced neurodegenerative disease. The dopamine-mediated swim to crawl locomotory transition behavior is exquisitely vulnerable to Mancozeb, with functional impairment preceding markers of neuronal structural damage. The damage is partially rescued in mutants lacking the divalent metal transporter, SMF-1, demonstrating that some, but not all, of the damage is mediated by manganese. Increasing concentrations of Mancozeb recruit additional behavioral dysfunction, notably serotonin-mediated egg-laying behavior, but without evident serotonergic neuronal structural damage. Thus, measurements of behavioral dysfunction are a sensitive early marker of fungicide toxicity that could be exploited to examine further mechanisms of neuron damage and possible therapeutic interventions. These results also provide important insight into the consequences of fungicide use on the ecological behavior of nematodes. PMID:23103283

  17. Protein-Induced Surface Structuring in Myelin Membrane Monolayers

    PubMed Central

    Rosetti, Carla M.; Maggio, Bruno

    2007-01-01

    Monolayers prepared from myelin conserve all the compositional complexity of the natural membrane when spread at the air-water interface. They show a complex pressure-dependent surface pattern that, on compression, changes from the coexistence of two liquid phases to a viscous fractal phase embedded in a liquid phase. We dissected the role of major myelin protein components, myelin basic protein (MBP), and Folch-Lees proteolipid protein (PLP) as crucial factors determining the structural dynamics of the interface. By analyzing mixtures of a single protein with the myelin lipids we found that MBP and PLP have different surface pressure-dependent behaviors. MBP stabilizes the segregation of two liquid phases at low pressures and becomes excluded from the film under compression, remaining adjacent to the interface. PLP, on the contrary, organizes a fractal-like pattern at all surface pressures when included in a monolayer of the protein-free myelin lipids but it remains mixed in the MBP-induced liquid phase. The resultant surface topography and dynamics is regulated by combined near to equilibrium and out-of-equilibrium effects. PLP appears to act as a surface skeleton for the whole components whereas MBP couples the structuring to surface pressure-dependent extrusion and adsorption processes. PMID:17905850

  18. A double-loop structure in the adaptive generalized predictive control algorithm for control of robot end-point contact force.

    PubMed

    Wen, Shuhuan; Zhu, Jinghai; Li, Xiaoli; Chen, Shengyong

    2014-09-01

    Robot force control is an essential issue in robotic intelligence. There is much high uncertainty when robot end-effector contacts with the environment. Because of the environment stiffness effects on the system of the robot end-effector contact with environment, the adaptive generalized predictive control algorithm based on quantitative feedback theory is designed for robot end-point contact force system. The controller of the internal loop is designed on the foundation of QFT to control the uncertainty of the system. An adaptive GPC algorithm is used to design external loop controller to improve the performance and the robustness of the system. Two closed loops used in the design approach realize the system׳s performance and improve the robustness. The simulation results show that the algorithm of the robot end-effector contacting force control system is effective. PMID:24973336

  19. A double-loop structure in the adaptive generalized predictive control algorithm for control of robot end-point contact force.

    PubMed

    Wen, Shuhuan; Zhu, Jinghai; Li, Xiaoli; Chen, Shengyong

    2014-09-01

    Robot force control is an essential issue in robotic intelligence. There is much high uncertainty when robot end-effector contacts with the environment. Because of the environment stiffness effects on the system of the robot end-effector contact with environment, the adaptive generalized predictive control algorithm based on quantitative feedback theory is designed for robot end-point contact force system. The controller of the internal loop is designed on the foundation of QFT to control the uncertainty of the system. An adaptive GPC algorithm is used to design external loop controller to improve the performance and the robustness of the system. Two closed loops used in the design approach realize the system׳s performance and improve the robustness. The simulation results show that the algorithm of the robot end-effector contacting force control system is effective.

  20. Formation of Chromosomal Domains by Loop Extrusion.

    PubMed

    Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A

    2016-05-31

    Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations-including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments-and makes specific predictions for the depletion of CTCF versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes. PMID:27210764

  1. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

    PubMed

    Völker, Jens; Gindikin, Vera; Klump, Horst H; Plum, G Eric; Breslauer, Kenneth J

    2012-04-01

    DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA

  2. Solutes alter the conformation of the ligand binding loops in outer membrane transporters.

    PubMed

    Kim, Miyeon; Xu, Qi; Murray, David; Cafiso, David S

    2008-01-15

    The binding and recognition of ligands by bacterial outer membrane transport proteins is mediated in part by interactions made through their extracellular loops. Here, site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy were used to examine the effect of stabilizing solutes on the extracellular loops in BtuB, the vitamin B12 transporter, and FecA, the ferric citrate transporter. EPR spectra from the extracellular loops of FecA and BtuB arise from dynamic backbone segments, and distance measurements made by double electron-electron resonance indicate that the second extracellular loop in BtuB samples a wide range of conformations. These conformations are dramatically restricted upon substrate binding. In addition, the EPR spectra from nitroxide labels attached to the extracellular loops in BtuB and FecA are highly sensitive to solutes, and at every site examined the motion of the label is significantly reduced in the presence of stabilizing osmolytes, such as polyethylene glycols. For the second extracellular loop in BtuB, the solute-induced structural changes are small, but they are sufficient to bring spin-labeled side chains into tertiary contact with other portions of the protein. The spectroscopic changes seen by SDSL suggest that high concentrations of stabilizing solutes, such as those used to generate membrane protein crystals, result in a more compact and ordered state of the protein than is seen under more physiological conditions.

  3. Quantitative Evaluation of Closed-Loop-Shaped Cardiomyocyte Network by Using Ring-Shaped Electrode

    NASA Astrophysics Data System (ADS)

    Nomura, Fumimasa; Kaneko, Tomoyuki; Hamada, Tomoyo; Hattori, Akihiro; Yasuda, Kenji

    2012-06-01

    Re-entry of excitation in the heart is one of the abnormal phenomena that causes lethal arrhythmia and is thought to be induced by the looped structure of the excitation conduction pathway. To evaluate the geometrical pattern dependence of electrophysiological results, we fabricated three models of cardiomyocyte networks and compared their beating frequencies (BFs), amplitudes of a depolarization peak, and field potential durations (FPDs). The set of different closed-loop-shaped network models from 3 to 8 mm in length showed the same BFs, amplitudes, and FPDs independent of their loop lengths, whereas the BFs and FPDs of 60 µm small clusters, and the FPDs of the 2 mm open-line-shaped network model were different from those of a closed-loop-shaped network model. These results indicate that the mm order larger size of clusters might create lower BFs, and the closed-loop-shaped model may generate longer FPDs. They also suggest the importance of spatial arrangement control of the cardoimyocyte community for reproducible measurement of electrophysiological properties of cardiomyocytes, especially control of the closed-loop formation, which might change the waveforms of FPDs depending on the difference in the geometry and conduction pathway of the cell network.

  4. The Orbital Structure of a Tidally Induced Bar

    NASA Astrophysics Data System (ADS)

    Gajda, Grzegorz; Łokas, Ewa L.; Athanassoula, E.

    2016-10-01

    Orbits are the key building blocks of any density distribution, and their study helps us understand the kinematical structure and the evolution of galaxies. Here, we investigate orbits in a tidally induced bar of a dwarf galaxy, using an N-body simulation of an initially disky dwarf galaxy orbiting a Milky Way-like host. After the first pericenter passage, a tidally induced bar forms in the stellar component of the dwarf. The bar evolution is different than in isolated galaxies and our analysis focuses on the period before it buckles. We study the orbits in terms of their dominant frequencies, which we calculate in a Cartesian coordinate frame rotating with the bar. Apart from the well-known x1 orbits, we find many other types, mostly with boxy shapes of various degree of elongation. Some of them are also near-periodic, admitting frequency ratios of 4/3, 3/2, and 5/3. The box orbits have various degrees of vertical thickness but only a relatively small fraction of those have banana (i.e., smile/frown) or infinity-symbol shapes in the edge-on view. In the very center we also find orbits known from the potential of triaxial ellipsoids. The elongation of the orbits grows with distance from the center of the bar in agreement with the variation of the shape of the density distribution. Our classification of orbits leads to the conclusion that more than 80% of them have boxy shapes, while only 8% have shapes of classical x1 orbits.

  5. Electrical stimulation induces IL-6 in skeletal muscle through extracellular ATP by activating Ca(2+) signals and an IL-6 autocrine loop.

    PubMed

    Bustamante, Mario; Fernández-Verdejo, Rodrigo; Jaimovich, Enrique; Buvinic, Sonja

    2014-04-15

    Interleukin-6 (IL-6) is an important myokine that is highly expressed in skeletal muscle cells upon exercise. We assessed IL-6 expression in response to electrical stimulation (ES) or extracellular ATP as a known mediator of the excitation-transcription mechanism in skeletal muscle. We examined whether the canonical signaling cascade downstream of IL-6 (IL-6/JAK2/STAT3) also responds to muscle cell excitation, concluding that IL-6 influences its own expression through a positive loop. Either ES or exogenous ATP (100 μM) increased both IL-6 expression and p-STAT3 levels in rat myotubes, a process inhibited by 100 μM suramin and 2 U/ml apyrase. ATP also evoked IL-6 expression in both isolated skeletal fibers and extracts derived from whole FDB muscles. ATP increased IL-6 release up to 10-fold. STAT3 activation evoked by ATP was abolished by the JAK2 inhibitor HBC. Blockade of secreted IL-6 with a neutralizing antibody or preincubation with the STAT3 inhibitor VIII reduced STAT3 activation evoked by extracellular ATP by 70%. Inhibitor VIII also reduced by 70% IL-6 expression evoked by ATP, suggesting a positive IL-6 loop. In addition, ATP increased up to 60% the protein levels of SOCS3, a negative regulator of the IL-6 signaling pathway. On the other hand, intracellular calcium chelation or blockade of IP3-dependent calcium signals abolished STAT3 phosphorylation evoked by either extracellular ATP or ES. These results suggest that expression of IL-6 in stimulated skeletal muscle cells is mediated by extracellular ATP and nucleotide receptors, involving IP3-dependent calcium signals as an early step that triggers a positive IL-6 autocrine loop.

  6. Electrical stimulation induces IL-6 in skeletal muscle through extracellular ATP by activating Ca2+ signals and an IL-6 autocrine loop

    PubMed Central

    Bustamante, Mario; Fernández-Verdejo, Rodrigo; Jaimovich, Enrique

    2014-01-01

    Interleukin-6 (IL-6) is an important myokine that is highly expressed in skeletal muscle cells upon exercise. We assessed IL-6 expression in response to electrical stimulation (ES) or extracellular ATP as a known mediator of the excitation-transcription mechanism in skeletal muscle. We examined whether the canonical signaling cascade downstream of IL-6 (IL-6/JAK2/STAT3) also responds to muscle cell excitation, concluding that IL-6 influences its own expression through a positive loop. Either ES or exogenous ATP (100 μM) increased both IL-6 expression and p-STAT3 levels in rat myotubes, a process inhibited by 100 μM suramin and 2 U/ml apyrase. ATP also evoked IL-6 expression in both isolated skeletal fibers and extracts derived from whole FDB muscles. ATP increased IL-6 release up to 10-fold. STAT3 activation evoked by ATP was abolished by the JAK2 inhibitor HBC. Blockade of secreted IL-6 with a neutralizing antibody or preincubation with the STAT3 inhibitor VIII reduced STAT3 activation evoked by extracellular ATP by 70%. Inhibitor VIII also reduced by 70% IL-6 expression evoked by ATP, suggesting a positive IL-6 loop. In addition, ATP increased up to 60% the protein levels of SOCS3, a negative regulator of the IL-6 signaling pathway. On the other hand, intracellular calcium chelation or blockade of IP3-dependent calcium signals abolished STAT3 phosphorylation evoked by either extracellular ATP or ES. These results suggest that expression of IL-6 in stimulated skeletal muscle cells is mediated by extracellular ATP and nucleotide receptors, involving IP3-dependent calcium signals as an early step that triggers a positive IL-6 autocrine loop. PMID:24518675

  7. Electrical stimulation induces IL-6 in skeletal muscle through extracellular ATP by activating Ca(2+) signals and an IL-6 autocrine loop.

    PubMed

    Bustamante, Mario; Fernández-Verdejo, Rodrigo; Jaimovich, Enrique; Buvinic, Sonja

    2014-04-15

    Interleukin-6 (IL-6) is an important myokine that is highly expressed in skeletal muscle cells upon exercise. We assessed IL-6 expression in response to electrical stimulation (ES) or extracellular ATP as a known mediator of the excitation-transcription mechanism in skeletal muscle. We examined whether the canonical signaling cascade downstream of IL-6 (IL-6/JAK2/STAT3) also responds to muscle cell excitation, concluding that IL-6 influences its own expression through a positive loop. Either ES or exogenous ATP (100 μM) increased both IL-6 expression and p-STAT3 levels in rat myotubes, a process inhibited by 100 μM suramin and 2 U/ml apyrase. ATP also evoked IL-6 expression in both isolated skeletal fibers and extracts derived from whole FDB muscles. ATP increased IL-6 release up to 10-fold. STAT3 activation evoked by ATP was abolished by the JAK2 inhibitor HBC. Blockade of secreted IL-6 with a neutralizing antibody or preincubation with the STAT3 inhibitor VIII reduced STAT3 activation evoked by extracellular ATP by 70%. Inhibitor VIII also reduced by 70% IL-6 expression evoked by ATP, suggesting a positive IL-6 loop. In addition, ATP increased up to 60% the protein levels of SOCS3, a negative regulator of the IL-6 signaling pathway. On the other hand, intracellular calcium chelation or blockade of IP3-dependent calcium signals abolished STAT3 phosphorylation evoked by either extracellular ATP or ES. These results suggest that expression of IL-6 in stimulated skeletal muscle cells is mediated by extracellular ATP and nucleotide receptors, involving IP3-dependent calcium signals as an early step that triggers a positive IL-6 autocrine loop. PMID:24518675

  8. Effect of DNA looping on the induction kinetics of the lac operon.

    PubMed

    Narang, Atul

    2007-08-21

    The induction of the lac operon follows cooperative kinetics. The first mechanistic model of these kinetics is the de facto standard in the modeling literature [Yagil, G., Yagil, E., 1971. On the relation between effector concentration and the rate of induced enzyme synthesis. Biophys. J. 11, 11-17]. Yet, subsequent studies have shown that the model is based on incorrect assumptions. Specifically, the repressor is a tetramer with four (not two) inducer-binding sites, and the operon contains two auxiliary operators (in addition to the main operator). Furthermore, these structural features are crucial for the formation of DNA loops, the key determinants of lac repression and induction. Indeed, the repression is determined almost entirely (>95%) by the looped complexes [Oehler, S., Eismann, E.R., Krämer, H., Müller-Hill, B., 1990. The three operators of the lac operon cooperate in repression. EMBO J. 9(4), 973-979], and the pronounced cooperativity of the induction curve hinges upon the existence of the looped complexes [Oehler, S., Alberti, S., Müller-Hill, B., 2006. Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction. Nucleic Acids Res. 34(2), 606-612]. Here, we formulate a model of lac induction taking due account of the tetrameric structure of the repressor and the existence of looped complexes. We show that: (1) The kinetics are significantly more cooperative than those predicted by the Yagil and Yagil model. The cooperativity is higher because the formation of looped complexes is easily abolished by repressor-inducer binding. (2) The model provides good fits to the repression data for cells containing wild-type tetrameric or mutant dimeric repressor, as well as the induction curves for 6 different strains of Escherichia coli. It also implies that the ratios of certain looped and non-looped complexes are independent of inducer and repressor levels, a conclusion that can be rigorously tested by gel electrophoresis. (3

  9. Bent helix formation between RNA hairpins with complementary loops.

    PubMed

    Marino, J P; Gregorian, R S; Csankovszki, G; Crothers, D M

    1995-06-01

    The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication. PMID:7539549

  10. Bent helix formation between RNA hairpins with complementary loops.

    PubMed

    Marino, J P; Gregorian, R S; Csankovszki, G; Crothers, D M

    1995-06-01

    The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication.

  11. Turbomachinery Design Quality Checks to Avoid Friction Induced Structural Failure

    NASA Technical Reports Server (NTRS)

    Moore, Jerry H.

    1999-01-01

    A unique configuration of the P&W SSME Alternate Fuel Turbopump turbine disk/blade assembly, combined with a severe thermal environment, resulted in several structural anomalies that were driven by frictional contact forces. Understanding the mechanics of these problems provides new quality checks for future turbo machinery designs. During development testing in 1997 of the SSME alternate fuel turbopump at Stennis Space Center, several potentially serious problems surfaced with the turbine disk/blade assembly that had not been experienced in extensive earlier testing. Changes to the operational thermal environment were noted based on analytical prediction of modifications that affected performance and on stationary thermal measurements adjacent to the rotor assembly. A detailed structural investigation was required to reveal the mechanism of distress induced by the change. The turbine disk experienced cracking in several locations due to increased thermal gradient induced stress during start and shutdown transients. This was easily predictable using standard analysis procedures and expected once the thermal environment was characterized. What was not expected was the curling of a piston ring used for blade axial retention in the disk, indentation of the axial face of the blade attachment by a spacer separating the first and second stage blades, and most significantly, galling and cracking of the blade root attachment that could have resulted in blade release. Past experience, in gas turbine environments, set a precedent of never relying on friction for help and to evaluate it only in specific instances where it was obvious that it would degrade capability. In each of the three cases above, friction proved to be a determining factor that pushed the components into an unsatisfactory mode of operation. The higher than expected temperatures and rapid thermal transients combined with friction to move beyond past experience. The turbine disk/blade assembly configuration

  12. Radiation-Induced Topological Disorder in Irradiated Network Structures

    SciTech Connect

    Hobbs, Linn W.

    2002-12-21

    This report summarizes results of a research program investigating the fundamental principles underlying the phenomenon of topological disordering in a radiation environment. This phenomenon is known popularly as amorphization, but is more formally described as a process of radiation-induced structural arrangement that leads in crystals to loss of long-range translational and orientational correlations and in glasses to analogous alteration of connectivity topologies. The program focus has been on a set compound ceramic solids with directed bonding exhibiting structures that can be described as networks. Such solids include SiO2, Si3N4, SiC, which are of interest to applications in fusion energy production, nuclear waste storage, and device manufacture involving ion implantation or use in radiation fields. The principal investigative tools comprise a combination of experimental diffraction-based techniques, topological modeling, and molecular-dynamics simulations that have proven a rich source of information in the preceding support period. The results from the present support period fall into three task areas. The first comprises enumeration of the rigidity constraints applying to (1) more complex ceramic structures (such as rutile, corundum, spinel and olivine structures) that exhibit multiply polytopic coordination units or multiple modes of connecting such units, (2) elemental solids (such as graphite, silicon and diamond) for which a correct choice of polytope is necessary to achieve correct representation of the constraints, and (3) compounds (such as spinel and silicon carbide) that exhibit chemical disorder on one or several sublattices. With correct identification of the topological constraints, a unique correlation is shown to exist between constraint and amorphizability which demonstrates that amorphization occurs at a critical constraint loss. The second task involves the application of molecular dynamics (MD) methods to topologically-generated models

  13. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

    PubMed

    Pan, Hu; Agarwalla, Sanjay; Moustakas, Demetri T; Finer-Moore, Janet; Stroud, Robert M

    2003-10-28

    RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.

  14. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  15. The EF Loop in Green Proteorhodopsin Affects Conformation and Photocycle dynamics

    PubMed Central

    Mehler, Michaela; Scholz, Frank; Ullrich, Sandra J.; Mao, Jiafei; Braun, Markus; Brown, Lynda J.; Brown, Richard C.D.; Fiedler, Sarah A.; Becker-Baldus, Johanna; Wachtveitl, Josef; Glaubitz, Clemens

    2013-01-01

    The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced 13C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins. PMID:23870260

  16. The EF loop in green proteorhodopsin affects conformation and photocycle dynamics.

    PubMed

    Mehler, Michaela; Scholz, Frank; Ullrich, Sandra J; Mao, Jiafei; Braun, Markus; Brown, Lynda J; Brown, Richard C D; Fiedler, Sarah A; Becker-Baldus, Johanna; Wachtveitl, Josef; Glaubitz, Clemens

    2013-07-16

    The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.

  17. The EF loop in green proteorhodopsin affects conformation and photocycle dynamics.

    PubMed

    Mehler, Michaela; Scholz, Frank; Ullrich, Sandra J; Mao, Jiafei; Braun, Markus; Brown, Lynda J; Brown, Richard C D; Fiedler, Sarah A; Becker-Baldus, Johanna; Wachtveitl, Josef; Glaubitz, Clemens

    2013-07-16

    The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins. PMID:23870260

  18. A Systematic Investigation of Structure/Function Requirements for the Apolipoprotein A-I/Lecithin Cholesterol Acyltransferase Interaction Loop of High-density Lipoprotein.

    PubMed

    Gu, Xiaodong; Wu, Zhiping; Huang, Ying; Wagner, Matthew A; Baleanu-Gogonea, Camelia; Mehl, Ryan A; Buffa, Jennifer A; DiDonato, Anthony J; Hazen, Leah B; Fox, Paul L; Gogonea, Valentin; Parks, John S; DiDonato, Joseph A; Hazen, Stanley L

    2016-03-18

    The interaction of lecithin-cholesterol acyltransferase (LCAT) with apolipoprotein A-I (apoA-I) plays a critical role in high-density lipoprotein (HDL) maturation. We previously identified a highly solvent-exposed apoA-I loop domain (Leu(159)-Leu(170)) in nascent HDL, the so-called "solar flare" (SF) region, and proposed that it serves as an LCAT docking site (Wu, Z., Wagner, M. A., Zheng, L., Parks, J. S., Shy, J. M., 3rd, Smith, J. D., Gogonea, V., and Hazen, S. L. (2007) Nat. Struct. Mol. Biol. 14, 861-868). The stability and role of the SF domain of apoA-I in supporting HDL binding and activation of LCAT are debated. Here we show by site-directed mutagenesis that multiple residues within the SF region (Pro(165), Tyr(166), Ser(167), and Asp(168)) of apoA-I are critical for both LCAT binding to HDL and LCAT catalytic efficiency. The critical role for possible hydrogen bond interaction at apoA-I Tyr(166) was further supported using reconstituted HDL generated from apoA-I mutants (Tyr(166) → Glu or Asn), which showed preservation in both LCAT binding affinity and catalytic efficiency. Moreover, the in vivo functional significance of NO2-Tyr(166)-apoA-I, a specific post-translational modification on apoA-I that is abundant within human atherosclerotic plaque, was further investigated by using the recombinant protein generated from E. coli containing a mutated orthogonal tRNA synthetase/tRNACUA pair enabling site-specific insertion of the unnatural amino acid into apoA-I. NO2-Tyr(166)-apoA-I, after subcutaneous injection into hLCAT(Tg/Tg), apoA-I(-/-) mice, showed impaired LCAT activation in vivo, with significant reduction in HDL cholesteryl ester formation. The present results thus identify multiple structural features within the solvent-exposed SF region of apoA-I of nascent HDL essential for optimal LCAT binding and catalytic efficiency.

  19. A Systematic Investigation of Structure/Function Requirements for the Apolipoprotein A-I/Lecithin Cholesterol Acyltransferase Interaction Loop of High-density Lipoprotein.

    PubMed

    Gu, Xiaodong; Wu, Zhiping; Huang, Ying; Wagner, Matthew A; Baleanu-Gogonea, Camelia; Mehl, Ryan A; Buffa, Jennifer A; DiDonato, Anthony J; Hazen, Leah B; Fox, Paul L; Gogonea, Valentin; Parks, John S; DiDonato, Joseph A; Hazen, Stanley L

    2016-03-18

    The interaction of lecithin-cholesterol acyltransferase (LCAT) with apolipoprotein A-I (apoA-I) plays a critical role in high-density lipoprotein (HDL) maturation. We previously identified a highly solvent-exposed apoA-I loop domain (Leu(159)-Leu(170)) in nascent HDL, the so-called "solar flare" (SF) region, and proposed that it serves as an LCAT docking site (Wu, Z., Wagner, M. A., Zheng, L., Parks, J. S., Shy, J. M., 3rd, Smith, J. D., Gogonea, V., and Hazen, S. L. (2007) Nat. Struct. Mol. Biol. 14, 861-868). The stability and role of the SF domain of apoA-I in supporting HDL binding and activation of LCAT are debated. Here we show by site-directed mutagenesis that multiple residues within the SF region (Pro(165), Tyr(166), Ser(167), and Asp(168)) of apoA-I are critical for both LCAT binding to HDL and LCAT catalytic efficiency. The critical role for possible hydrogen bond interaction at apoA-I Tyr(166) was further supported using reconstituted HDL generated from apoA-I mutants (Tyr(166) → Glu or Asn), which showed preservation in both LCAT binding affinity and catalytic efficiency. Moreover, the in vivo functional significance of NO2-Tyr(166)-apoA-I, a specific post-translational modification on apoA-I that is abundant within human atherosclerotic plaque, was further investigated by using the recombinant protein generated from E. coli containing a mutated orthogonal tRNA synthetase/tRNACUA pair enabling site-specific insertion of the unnatural amino acid into apoA-I. NO2-Tyr(166)-apoA-I, after subcutaneous injection into hLCAT(Tg/Tg), apoA-I(-/-) mice, showed impaired LCAT activation in vivo, with significant reduction in HDL cholesteryl ester formation. The present results thus identify multiple structural features within the solvent-exposed SF region of apoA-I of nascent HDL essential for optimal LCAT binding and catalytic efficiency. PMID:26797122

  20. Leading QCD-induced four-loop contributions to the β-function of the Higgs self-coupling in the SM and vacuum stability

    NASA Astrophysics Data System (ADS)

    Chetyrkin, K. G.; Zoller, M. F.

    2016-06-01

    We present analytical results for the leading top-Yukawa and QCD contribution to the β-function for the Higgs self-coupling λ of the Standard Model at four-loop level, namely the part ∝ y t 4 g s 6 independently confirming a result given in [1]. We also give the contribution ∝ y t 2 g s 6 of the anomalous dimension of the Higgs field as well as the terms ∝ y t g s 8 to the top-Yukawa β-function which can also be derived from the anomalous dimension of the top quark mass. We compare the results with the RG functions of the correlators of two and four scalar currents in pure QCD and find a new relation between the anomalous dimension γ 0 of the QCD vacuum energy and the anomalous dimension γ m SS appearing in the RG equation of the correlator of two scalar currents. Together with the recently computed top-Yukawa and QCD contributions to β gs [2, 3] the β-functions presented here constitute the leading four-loop contributions to the evolution of the Higgs self-coupling. A numerical estimate of these terms at the scale of the top-quark mass is presented as well as an analysis of the impact on the evolution of λ up to the Planck scale and the vacuum stability problem.

  1. The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.

    PubMed

    Alexeeva, Marina; Åberg, Espen; Engh, Richard A; Rothweiler, Ulli

    2015-05-01

    Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery. PMID:25945585

  2. A PH-INDUCED STRUCTURAL CHANGE IN BROMEGRASS MOSAIC VIRUS.

    PubMed

    INCARDONA, N L; KAESBERG, P

    1964-01-01

    Bromegrass mosaic virus undergoes a reversible decrease in its sedimentation coefficient when the pH is raised above pH 6.7. At pH 6 the sedimentation coefficient is 87 S, at pH 7 it is 79 S. Intrinsic viscosities determined at pH 6 and 7 are 3.64 and 5.5 x 10(-2) dl/gm. Diffusion coefficients are 1.56 x 10(-7) cm(2)/sec. and 1.44 x 10(-7) cm(2)/sec., respectively. Radii of gyration, measured by x-ray scattering, are 106 and 128 A. However, appropriate combination of sedimentation, diffusion, and viscosity coefficients at pH 6 and 7 yield the same molecular weight. Also, the zero-angle value of x-ray-scattered intensity, which is a function of molecular weight, is the same at the two pH's. These results suggest that bromegrass mosaic virus particles undergo a pH-induced change in structure. This change causes, among other things, an increase in the susceptibility of the particles to degradation by pancreatic ribonuclease. The shape of the titration curve between pH 6.3 and 6.9 is anomalous.

  3. Femtosecond laser-induced periodic surface structures on silica

    SciTech Connect

    Hoehm, S.; Rosenfeld, A.; Krueger, J.; Bonse, J.

    2012-07-01

    The formation of laser-induced periodic surface structures (LIPSS) on two different silica polymorphs (single-crystalline synthetic quartz and commercial fused silica glass) upon irradiation in air with multiple linearly polarized single- and double-fs-laser pulse sequences ({tau} = 150 fs pulse duration, {lambda} = 800 nm center wavelength, temporal pulse separation {Delta}t < 40 ps) is studied experimentally and theoretically. Two distinct types of fs-LIPSS [so-called low-spatial-frequency LIPSS (LSFL) and high-spatial-frequency LIPSS (HSFL)] with different spatial periods and orientations were identified. Their appearance was characterized with respect to the experimental parameters peak laser fluence and number of laser pulses per spot. Additionally, the 'dynamics' of the LIPSS formation was addressed in complementary double-fs-pulse experiments with varying delays, revealing a characteristic change of the LSFL periods. The experimental results are interpreted on the basis of a Sipe-Drude model considering the carrier dependence of the optical properties of fs-laser excited silica. This new approach provides an explanation of the LSFL orientation parallel to the laser beam polarisation in silica - as opposed to the behaviour of most other materials.

  4. Loop quantum cosmology in 2 +1 dimension

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2014-12-01

    As a first step to generalize the structure of loop quantum cosmology to the theories with the spacetime dimension other than four, the isotropic model of loop quantum cosmology in 2 +1 dimension is studied in this paper. We find that the classical big bang singularity is again replaced by a quantum bounce in the model. The similarities and differences between the (2 +1 )-dimensional model and the (3 +1 )-dimensional one are also discussed.

  5. FINITE ELEMENT MODELS FOR COMPUTING SEISMIC INDUCED SOIL PRESSURES ON DEEPLY EMBEDDED NUCLEAR POWER PLANT STRUCTURES.

    SciTech Connect

    XU, J.; COSTANTINO, C.; HOFMAYER, C.

    2006-06-26

    PAPER DISCUSSES COMPUTATIONS OF SEISMIC INDUCED SOIL PRESSURES USING FINITE ELEMENT MODELS FOR DEEPLY EMBEDDED AND OR BURIED STIFF STRUCTURES SUCH AS THOSE APPEARING IN THE CONCEPTUAL DESIGNS OF STRUCTURES FOR ADVANCED REACTORS.

  6. Modeling loop entropy.

    PubMed

    Chirikjian, Gregory S

    2011-01-01

    Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting "the" tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own. Quantifying the relative disorder in the folded and unfolded ensembles as an entropy difference may therefore shed light on the folding process. One issue that clouds discussions of "entropy" is that many different kinds of entropy can be defined: entropy associated with overall translational and rotational Brownian motion, configurational entropy, vibrational entropy, conformational entropy computed in internal or Cartesian coordinates (which can even be different from each other), conformational entropy computed on a lattice, each of the above with different solvation and solvent models, thermodynamic entropy measured experimentally, etc. The focus of this work is the conformational entropy of coil/loop regions in proteins. New mathematical modeling tools for the approximation of changes in conformational entropy during transition from unfolded to folded ensembles are introduced. In particular, models for computing lower and upper bounds on entropy for polymer models of polypeptide coils both with and without end constraints are presented. The methods reviewed here include kinematics (the mathematics of rigid-body motions), classical statistical mechanics, and information theory.

  7. Plasma Loops in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Bray, R. J.; Cram, L. E.; Durrant, C.; Loughhead, R. E.

    1991-07-01

    A comprehensive account of the properties of plasma loops, the fundamental structural elements of the solar corona. Plasma loops cover a wide range of sizes and range in temperature from tens of thousands to millions of degrees. They not only define the structure of individual active regions but connect different active regions--even across the solar equator. Loops also play an integral and decisive role in the enormous solar explosions called flares. Over recent years a wealth of space and ground-based observations of loops has been obtained in various widely-spaced regions of the electromagnetic spectrum. In this book the authors have selected the best observational material from the literature on which to base a detailed account of the properties of flare and non-flare loops. The book also explores the larger implications of the loop structures for our understanding of solar and stellar coronae. The text is enhanced by a large number of illustrations and unique and beautiful photographs obtained from the ground and from space.

  8. OBSERVING THE FINE STRUCTURE OF LOOPS THROUGH HIGH-RESOLUTION SPECTROSCOPIC OBSERVATIONS OF CORONAL RAIN WITH THE CRISP INSTRUMENT AT THE SWEDISH SOLAR TELESCOPE

    SciTech Connect

    Antolin, P.; Rouppe van der Voort, L. E-mail: v.d.v.l.rouppe@astro.uio.no

    2012-02-01

    Observed in cool chromospheric lines, such as H{alpha} or Ca II H, coronal rain corresponds to cool and dense plasma falling from coronal heights. Considered as a peculiar sporadic phenomenon of active regions, it has not received much attention since its discovery more than 40 years ago. Yet, it has been shown recently that a close relationship exists between this phenomenon and the coronal heating mechanism. Indeed, numerical simulations have shown that this phenomenon is most likely due to a loss of thermal equilibrium ensuing from a heating mechanism acting mostly toward the footpoints of loops. We present here one of the first high-resolution spectroscopic observations of coronal rain, performed with the CRisp Imaging Spectro Polarimeter (CRISP) instrument at the Swedish Solar Telescope. This work constitutes the first attempt to assess the importance of coronal rain in the understanding of the coronal magnetic field in active regions. With the present resolution, coronal rain is observed to literally invade the entire field of view. A large statistical set is obtained in which dynamics (total velocities and accelerations), shapes (lengths and widths), trajectories (angles of fall of the blobs), and thermodynamic properties (temperatures) of the condensations are derived. Specifically, we find that coronal rain is composed of small and dense chromospheric cores with average widths and lengths of {approx}310 km and {approx}710 km, respectively, average temperatures below 7000 K, displaying a broad distribution of falling speeds with an average of {approx}70 km s{sup -1}, and accelerations largely below the effective gravity along loops. Through estimates of the ion-neutral coupling in the blobs we show that coronal rain acts as a tracer of the coronal magnetic field, thus supporting the multi-strand loop scenario, and acts as a probe of the local thermodynamic conditions in loops. We further elucidate its potential in coronal heating. We find that the cooling

  9. Thermal power loops

    NASA Technical Reports Server (NTRS)

    Gottschlich, Joseph M.; Richter, Robert

    1991-01-01

    The concept of a thermal power loop (TPL) to transport thermal power over relatively large distances is presented as an alternative to heat pipes and their derivatives. The TPL is compared to heat pipes, and capillary pumped loops with respect to size, weight, conservation of thermal potential, start-up, and 1-g testing capability. Test results from a proof of feasibility demonstrator at the NASA JPL are discussed. This analysis demonstrates that the development of specific thermal power loops will result in substantial weight and cost savings for many spacecraft.

  10. Multiprotein DNA Looping

    NASA Astrophysics Data System (ADS)

    Vilar, Jose M. G.; Saiz, Leonor

    2006-06-01

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  11. Empirical potential simulations of interstitial dislocation loops in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Le Prioux, Arno; Fossati, Paul; Maillard, Serge; Jourdan, Thomas; Maugis, Philippe

    2016-10-01

    Stoichiometric circular shaped interstitial dislocation loop energies are calculated in stoichiometric UO2 by empirical potential simulation. The Burgers vector directions studied are <110> and <111>. The main structural properties of each type of interstitial dislocation loop are determined, including stacking fault energy. Defect energies are compared and a maximum size for stable <111> dislocation loops before transition to <110> dislocation loops is given. A model of dislocation loop energy based on elasticity theory is then fitted on the basis of these simulation results.

  12. LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins

    PubMed Central

    Li, Shuai Cheng; Li, Ming

    2013-01-01

    Abstract Modeling loops is a necessary step in protein structure determination, even with experimental nuclear magnetic resonance (NMR) data, it is widely known to be difficult. Database techniques have the advantage of producing a higher proportion of predictions with subangstrom accuracy when compared with ab initio techniques, but the disadvantage of also producing a higher proportion of clashing or highly inaccurate predictions. We introduce LoopWeaver, a database method that uses multidimensional scaling to achieve better, clash-free placement of loops obtained from a database of protein structures. This allows us to maintain the above-mentioned advantage while avoiding the disadvantage. Test results show that we achieve significantly better results than all other methods, including Modeler, Loopy, SuperLooper, and Rapper, before refinement. With refinement, our results (LoopWeaver and Loopy consensus) are better than ROSETTA, with 0.42 Å RMSD on average for 206 length 6 loops, 0.64 Å local RMSD for 168 length 7 loops, 0.81Å RMSD for 117 length 8 loops, and 0.98 Å RMSD for length 9 loops, while ROSETTA has 0.55, 0.79, 1.16, 1.42, respectively, at the same average time limit (3 hours). When we allow ROSETTA to run for over a week, it approaches, but does not surpass, our accuracy. PMID:23461572

  13. Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

    NASA Astrophysics Data System (ADS)

    Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

    2004-04-01

    We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  14. Irradiation-Induced Formation of Nanocrystallites with C15 Laves Phase Structure in bcc Iron

    NASA Astrophysics Data System (ADS)

    Marinica, M.-C.; Willaime, F.; Crocombette, J.-P.

    2012-01-01

    A three-dimensional periodic structure is proposed for self-interstitial clusters in body-centered-cubic metals, as opposed to the conventional two-dimensional loop morphology. The underlying crystal structure corresponds to the C15 Laves phase. Using density functional theory and interatomic potential calculations, we demonstrate that in α-iron these C15 aggregates are highly stable and immobile and that they exhibit large antiferromagnetic moments. They form directly in displacement cascades, and they can grow by capturing self-interstitials. They thus constitute an important new element to account for when predicting the microstructural evolution of iron base materials under irradiation.

  15. Introduction to Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  16. Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc

    PubMed Central

    Stettner, Eva; Jeffers, Scott Allen; Pérez-Vargas, Jimena; Pehau-Arnaudet, Gerard; Tortorici, M. Alejandra; Jestin, Jean-Luc; England, Patrick; Tischler, Nicole D.; Rey, Félix A.

    2016-01-01

    Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single “fusion loop”. We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal “tail” that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens. PMID:27783711

  17. CD5 Binds to Interleukin-6 and Induces a Feed-Forward Loop with the Transcription Factor STAT3 in B Cells to Promote Cancer.

    PubMed

    Zhang, Chunyan; Xin, Hong; Zhang, Wang; Yazaki, Paul J; Zhang, Zhifang; Le, Keith; Li, Wenzhao; Lee, Heehyoung; Kwak, Larry; Forman, Stephen; Jove, Richard; Yu, Hua

    2016-04-19

    The participation of a specific subset of B cells and how they are regulated in cancer is unclear. Here, we demonstrate that the proportion of CD5(+) relative to interleukin-6 receptor α (IL-6Rα)-expressing B cells was greatly increased in tumors. CD5(+) B cells responded to IL-6 in the absence of IL-6Rα. IL-6 directly bound to CD5, leading to activation of the transcription factor STAT3 via gp130 and its downstream kinase JAK2. STAT3 upregulated CD5 expression, thereby forming a feed-forward loop in the B cells. In mouse tumor models, CD5(+) but not CD5(-) B cells promoted tumor growth. CD5(+) B cells also showed activation of STAT3 in multiple types of human tumor tissues. Thus, our findings demonstrate a critical role of CD5(+) B cells in promoting cancer.

  18. Replacing a piece of loop-structure in the substrate-binding groove of Aspergillus usamii β-mannanase, AuMan5A, to improve its enzymatic properties by rational design.

    PubMed

    Dong, Yun Hai; Li, Jian Fang; Hu, Die; Yin, Xin; Wang, Chun Juan; Tang, Shi Han; Wu, Min Chen

    2016-05-01

    To perfect the enzymatic properties of AuMan5A, a mesophilic glycoside hydrolase (GH) family 5 β-mannanase from Aspergillus usamii, its loop-structure substitution was carried out by rational design and followed by megaprimer PCR. Based on the structural analysis and enzymatic property comparison of various β-mannanases, a piece of loop-structure with seven amino acids between two β-strands (βD and βE) in the substrate-binding groove, named "Loop DE," was speculated to be correlative to the thermostability and catalytic efficiency of GH family 5 β-mannanases. Therefore, three AuMan5A's mutants, AuMan5A-Af, AuMan5A-An, and AuMan5A-Th, were designed by substituting a Loop DE sequence ((316)KSPDGGN(322)) of AuMan5A with the corresponding sequences of other three family 5 β-mannanases, respectively. Then, the mutant-encoding genes, Auman5A-Af, Auman5A-An, and Auman5A-Th, were constructed as designed theoretically and then expressed in Pichia pastoris GS115. The expressed recombinant AuMan5A-Af (re-AuMan5A-Af) displayed the temperature optimum (T opt) of 75 °C, T m value of 76.6 °C and half-life (t 1/2) of 480 min at 70 °C, which were 10 and 12.1 °C higher and 48-fold longer than those of re-AuMan5A, respectively. Its catalytic efficiency (k cat/K m) was 12.7-fold that of re-AuMan5A. What is more, the site-directed mutagenesis of D320G in AuMan5A-Af was performed. The T opt and t 1/2 of expressed re-AuMan5A-Af(D320G) decreased to 70 °C and 40 min, respectively, while its k cat/K m was only 35 % of that of re-AuMan5A-Af. These results demonstrated that the mutation of G320 (in AuMan5A) into D320 (in AuMan5A-Af) through Loop DE substitution was mainly responsible for the thermostability and catalytic efficiency improvement of AuMan5A-Af.

  19. Mitotic chromosome compaction via active loop extrusion

    NASA Astrophysics Data System (ADS)

    Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

    During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

  20. Perturbation Theory at Eight Loops: Novel Structures and the Breakdown of Manifest Conformality in N=4 Supersymmetric Yang-Mills Theory.

    PubMed

    Bourjaily, Jacob L; Heslop, Paul; Tran, Vuong-Viet

    2016-05-13

    We use the soft-collinear bootstrap to construct the 8-loop integrand for the 4-point amplitude and 4-stress-tensor correlation function in planar maximally supersymmetric Yang-Mills theory. Both have a unique representation in terms of planar, conformal integrands grouped according to a hidden symmetry discovered for correlation functions. The answer we find exposes a fundamental tension between manifest locality and planarity with manifest conformality not seen at lower loops. For the first time, the integrand must include terms that are finite even on-shell and terms that are divergent even off-shell (so-called pseudoconformal integrals). We describe these novelties and their consequences in this Letter, and we make the full correlator and amplitude available as part of the Supplemental Material. PMID:27232016

  1. Chromatin structure and ionizing-radiation-induced chromosome aberrations

    SciTech Connect

    Muehlmann-Diaz, M.C.

    1993-01-01

    The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 10[sup 5] copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G[sub 0], the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes.

  2. Blind loop syndrome

    MedlinePlus

    ... operations for extreme obesity As a complication of inflammatory bowel disease Diseases such as diabetes or scleroderma may slow down movement in a segment of the intestine, leading to blind loop syndrome.

  3. CALCIUM-INDUCED SUPRAMOLECULAR STRUCTURES IN THE CALCIUM CASEINATE SYSTEM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular details deciphering the spontaneous calcium-induced protein aggregation process in the calcium caseinate system remain obscure. Understanding this complex process could lead to potential new applications of this important food ingredient. In this work, we studied calcium-induced supra...

  4. Investigation of the influence of capillary effect on operation of the loop heat pipe

    NASA Astrophysics Data System (ADS)

    Mikielewicz, Dariusz; Błauciak, Krzysztof

    2014-09-01

    In the paper presented are studies on the investigation of the capillary forces effect induced in the porous structure of a loop heat pipe using water and ethanol ad test fluids. The potential application of such effect is for example in the evaporator of the domestic micro-CHP unit, where the reduction of pumping power could be obtained. Preliminary analysis of the results indicates water as having the best potential for developing the capillary effect.

  5. Modeling RNA loops using sequence homology and geometric constraints

    PubMed Central

    Schudoma, Christian; May, Patrick; Walther, Dirk

    2010-01-01

    Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface. Availability and Implementation: The application was implemented in Python, MySQL and Apache. A web interface to the database and loop modeling application is freely available at http://rloom.mpimp-golm.mpg.de Contact: schudoma@mpimp-golm.mpg.de; may@mpimp-golm.mpg.de; walther@mpimp-golm.mpg.de PMID:20427516

  6. Sequence diversity and ligand-induced structural rearrangements of viper hyaluronidase.

    PubMed

    Bharathi, A Christian; Yadav, Pradeep Kumar; Syed Ibrahim, B

    2016-04-01

    Hyaluronidases (Hyals) are a class of carbohydrate-active enzyme involved in angiogenesis, cancer proliferation, tumour growth and venom spreading. Functionally significant Hyals are responsible for the fast spreading of venom to the target site of action. The absence of molecular diversity and the structural and functional behaviour of snake venom Hyals was the inspiration for the objective of this study. Echis pyramidum leakeyi hyaluronidase (EHY)-based phylogenetic analysis showed the existence of two functional groups of Hyals which had diverged from the coral snake (the ancestor). The structure was modelled and it was found that the E-loop region (211-224 AA) was only present in EHY compared to the templates which may account for the significant function of viper Hyal. The best interacting ligands were screened from the selected plant derivatives and MYR consisted of better pharmacophore features (AADDRRR) in comparison with other ligands. Furthermore, the HOMO, LUMO, and MO energies and energy gaps of CGA, MIM and MYR were calculated by DFT analysis. EHY-ligand complex stability and interactions were investigated through MD simulation and FEL analysis. These revealed that MIM and MYR or their derivative compounds could be prominent lead molecules for both EHY and other eukaryotic Hyals. PCA analysis of both the non-ligated and ligated forms confirmed that loop-III (86-96 AA) and E-loop region structural rearrangements were essential for the association and dissociation process of the substrate. Particularly, ARG92 and LYS219 are determined as important key residues from the conformational changes. These regions' dynamic behaviour can be associated with HA binding and the catalytic function of EHY. This result can extend our knowledge of viper Hyal functional behaviour and provides structural insight to target eukaryotic Hyals as forthcoming drug targets in cancer treatment and venom spreading. PMID:26867694

  7. Faraday induction when a loop grazes a magnet

    NASA Astrophysics Data System (ADS)

    Binder, P.-M.; Holub, Eric M.; Roberts, Marc F.; Wasser, Valerie K.

    2016-07-01

    We perform an experiment to detect electromagnetic induction when a magnet and a loop approach each other in grazing motion, oriented parallel to each other and with one magnet pole pointing at the loop. A weak emf is detected with a three-peak structure, which we explain. We also describe how a more complicated structure can arise.

  8. Saccade learning with concurrent cortical and subcortical basal ganglia loops

    PubMed Central

    N'Guyen, Steve; Thurat, Charles; Girard, Benoît

    2014-01-01

    The Basal Ganglia (BG) is a central structure involved in multiple cortical and subcortical loops. Some of these loops are believed to be responsible for saccade target selection. We study here how the very specific structural relationships of these saccadic loops can affect the ability of learning spatial and feature-based tasks. We propose a model of saccade generation with reinforcement learning capabilities based on our previous BG and superior colliculus models. It is structured around the interactions of two parallel cortico-basal loops and one tecto-basal loop. The two cortical loops separately deal with spatial and non-spatial information to select targets in a concurrent way. The subcortical loop is used to make the final target selection leading to the production of the saccade. These different loops may work in concert or disturb each other regarding reward maximization. Interactions between these loops and their learning capabilities are tested on different saccade tasks. The results show the ability of this model to correctly learn basic target selection based on different criteria (spatial or not). Moreover the model reproduces and explains training dependent express saccades toward targets based on a spatial criterion. Finally, the model predicts that in absence of prefrontal control, the spatial loop should dominate. PMID:24795615

  9. The importance of slow motions for protein functional loops

    NASA Astrophysics Data System (ADS)

    Skliros, Aris; Zimmermann, Michael T.; Chakraborty, Debkanta; Saraswathi, Saras; Katebi, Ataur R.; Leelananda, Sumudu P.; Kloczkowski, Andrzej; Jernigan, Robert L.

    2012-02-01

    Loops in proteins that connect secondary structures such as alpha-helix and beta-sheet, are often on the surface and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been studied much in the context of the whole structure and its overall motions, especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures (Cα atoms only) to solve the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes is investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But overall only a relatively few loops move in coordination with the dominant slow modes of motion, and these are often closely related to function.

  10. Evaluation of Lightning Induced Effects in a Graphite Composite Fairing Structure

    NASA Technical Reports Server (NTRS)

    Trout, Dawn H.; Stanley, James E.; Wahid, Parveen F.

    2011-01-01

    Defining the electromagnetic environment inside a graphite composite fairing due to near-by lightning strikes is of interest to spacecraft developers. This effort develops a transmission-line-matrix (TLM) model with a CST Microstripes to examine induced voltages. on interior wire loops in a composite fairing due to a simulated near-by lightning strike. A physical vehicle-like composite fairing test fixture is constructed to anchor a TLM model in the time domain and a FEKO method of moments model in the frequency domain. Results show that a typical graphite composite fairing provides adequate shielding resulting in a significant reduction in induced voltages on high impedance circuits despite minimal attenuation of peak magnetic fields propagating through space in near-by lightning strike conditions.

  11. Structural Characterizations of Glycerol Kinase: Unraveling Phosphorylation-Induced Long-Range Activation

    SciTech Connect

    Yeh, Joanne I.; Kettering, Regina; Saxl, Ruth; Bourand, Alexa; Darbon, Emmanuelle; Joly, Nathalie; Briozzo, Pierre; Deutscher, Josef

    2009-09-11

    Glycerol metabolism provides a central link between sugar and fatty acid catabolism. In most bacteria, glycerol kinase plays a crucial role in regulating channel/facilitator-dependent uptake of glycerol into the cell. In the firmicute Enterococcus casseliflavus, this enzyme's activity is enhanced by phosphorylation of the histidine residue (His232) located in its activation loop, approximately 25 A from its catalytic cleft. We reported earlier that some mutations of His232 altered enzyme activities; we present here the crystal structures of these mutant GlpK enzymes. The structure of a mutant enzyme with enhanced enzymatic activity, His232Arg, reveals that residues at the catalytic cleft are more optimally aligned to bind ATP and mediate phosphoryl transfer. Specifically, the position of Arg18 in His232Arg shifts by approximately 1 A when compared to its position in wild-type (WT), His232Ala, and His232Glu enzymes. This new conformation of Arg18 is more optimally positioned at the presumed gamma-phosphate location of ATP, close to the glycerol substrate. In addition to structural changes exhibited at the active site, the conformational stability of the activation loop is decreased, as reflected by an approximately 35% increase in B factors ('thermal factors') in a mutant enzyme displaying diminished activity, His232Glu. Correlating conformational changes to alteration of enzymatic activities in the mutant enzymes identifies distinct localized regions that can have profound effects on intramolecular signal transduction. Alterations in pairwise interactions across the dimer interface can communicate phosphorylation states over 25 A from the activation loop to the catalytic cleft, positioning Arg18 to form favorable interactions at the beta,gamma-bridging position with ATP. This would offset loss of the hydrogen bonds at the gamma-phosphate of ATP during phosphoryl transfer to glycerol, suggesting that appropriate alignment of the second substrate of glycerol kinase

  12. Femtosecond laser-induced periodic surface structure formation on tungsten

    SciTech Connect

    Vorobyev, A. Y.; Guo Chunlei

    2008-09-15

    In this paper, we demonstrate the generation of periodic surface structures on a technologically important material, tungsten, at both 400 and 800 nm, despite that the table values of dielectric constants for tungsten at these two wavelengths suggest the absence of surface plasmons, a wave necessary for forming periodic structures on metals. Furthermore, we find that the structure periods formed on tungsten are significantly less than the laser wavelengths. We believe that the dielectric constants of tungsten change significantly due to intense laser pulse heating and surface structuring and roughening at nanometer scales, permitting surface plasmon excitation and periodic structure formation.

  13. Structure-function studies of PANDER, an islet specific cytokine inducing cell death of insulin-secreting beta cells.

    PubMed

    Yang, Jichun; Gao, Zhiyong; Robert, Claudia E; Burkhardt, Brant R; Gaweska, Helena; Wagner, Amary; Wu, Jianmei; Greene, Scott R; Young, Robert A; Wolf, Bryan A

    2005-08-30

    PANDER (pancreatic derived factor, FAM3B) is a novel cytokine, present in insulin secretory granules, that induces apoptosis of alpha and beta cells of mouse, rat, and human islets in a dose- and time-dependent manner, and may be implicated in diabetes. PANDER has the predicted secondary structure of 4 alpha-helical bundles with an up-up-down-down topology, and two disulfide bonds. Eleven mutated PANDERs were constructed and expressed in beta-TC3 cells to identify the essential region of PANDER involved in beta-cell death. Beta-cell function was assessed by assays of cell viability and insulin secretion. Based on quantitative real-time RT-PCR all mutant PANDERs had similar mRNA expression levels in beta-TC3 cells. Immunoblotting showed that ten of eleven mutant PANDER proteins were synthesized and detected in beta-TC3 cells. A mutant PANDER with no signal peptide, however, was not expressed. Truncation of helix D alone caused a 40-50% decrease in PANDER's activity, while truncation of both helices C and D resulted in a 75% loss of activity. In contrast, truncation of the N-terminus of PANDER (helix A, the loop between helices A and B, and the first two cysteines) had no effect on PANDER-induced beta-cell death. The third and fourth cysteines of PANDER, C91 and C229, were shown to form one disulfide bond and be functionally important. Finally, the region between Cys91 and Phe152 constitutes the active part of PANDER, based on the demonstration that mutants with truncation of helix B or C caused decreased beta-cell death and did not inhibit insulin secretion, as compared to wild-type PANDER. Hence, helices B and C and the second disulfide bond of PANDER are essential for PANDER-induced beta-cell death.

  14. Modulation of DNA loop lifetimes by the free energy of loop formation

    PubMed Central

    Chen, Yi-Ju; Johnson, Stephanie; Mulligan, Peter; Spakowitz, Andrew J.; Phillips, Rob

    2014-01-01

    Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system’s deformation free energy. We explain this observation by transition state theory and model the DNA–protein complex as an effective worm-like chain with twist. We introduce a finite protein–DNA binding interaction length, in competition with the characteristic DNA deformation length scale, as the physical origin of the previously unidentified loop dissociation dynamics observed here, and discuss the robustness of this behavior to perturbations in several polymer parameters. PMID:25411314

  15. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity

    PubMed Central

    Ayres, Cory M.; Scott, Daniel R.; Corcelli, Steven A.; Baker, Brian M.

    2016-01-01

    Complementarity determining region (CDR) loop flexibility has been suggested to play an important role in the selection and binding of ligands by T cell receptors (TCRs) of the cellular immune system. However, questions remain regarding the role of loop motion in TCR binding, and crystallographic structures have raised questions about the extent to which generalizations can be made. Here we studied the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5. We found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity. While the loops of A6 move rapidly in an uncorrelated fashion, those of DMF5 are substantially less mobile. Accordingly, the mechanisms of binding and cross-reactivity are very different between the two TCRs: whereas A6 relies on conformational selection to select and bind different ligands, DMF5 uses a more rigid, permissive architecture with greater reliance on slower motions or induced-fit. In addition to binding site flexibility, we also explored whether ligand-binding resulted in common dynamical changes in A6 and DMF5 that could contribute to TCR triggering. Although binding-linked motional changes propagated throughout both receptors, no common features were observed, suggesting that changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling. PMID:27118724

  16. Structural explanation for allolactose (lac operon inducer) synthesis by lacZ β-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor.

    PubMed

    Wheatley, Robert W; Lo, Summie; Jancewicz, Larisa J; Dugdale, Megan L; Huber, Reuben E

    2013-05-01

    β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2',2″-nitrilotriethanol) and L-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795-803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution.

  17. Structural Explanation for Allolactose (lac Operon Inducer) Synthesis by lacZ β-Galactosidase and the Evolutionary Relationship between Allolactose Synthesis and the lac Repressor

    PubMed Central

    Wheatley, Robert W.; Lo, Summie; Jancewicz, Larisa J.; Dugdale, Megan L.; Huber, Reuben E.

    2013-01-01

    β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2′,2″-nitrilotriethanol) and l-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795–803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution. PMID:23486479

  18. Structural explanation for allolactose (lac operon inducer) synthesis by lacZ β-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor.

    PubMed

    Wheatley, Robert W; Lo, Summie; Jancewicz, Larisa J; Dugdale, Megan L; Huber, Reuben E

    2013-05-01

    β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2',2″-nitrilotriethanol) and L-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795-803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution. PMID:23486479

  19. Structure and stability of variants of the sarcin-ricin loop of 28S rRNA: NMR studies of the prokaryotic SRL and a functional mutant.

    PubMed Central

    Seggerson, K; Moore, P B

    1998-01-01

    NMR has been used to examine the conformational properties of two variants of the sarcin-ricin loop (SRL) from eukaryotic 28S rRNA, which is essential for elongation factor interactions with the ribosome: (1) its bacterial homologue, which lacks two of the bases that flank the conserved 12-nt sequence in the middle of the SRL, but which is functionally equivalent, and (2) a functionally active variant of the eukaryotic SRL in which the bulged G within the conserved sequence is replaced by an A. The data indicate that, although the bacterial SRL is less stable than the eukaryotic SRL, its conformation is closely similar. Furthermore, even though replacement of the bulged G in the SRL with an A seriously destabilizes the center of the loop, its effect on the overall conformation of the SRL appears to be modest. In the course of this work, it was serendipitously discovered that at neutral pH, the C8 proton of the bulged G, in both PRO-SRL and E73, exchanges about 10 times faster than it does in GMP. PMID:9769095

  20. Void growth by dislocation-loop emission

    NASA Astrophysics Data System (ADS)

    Ahn, D. C.; Sofronis, P.; Kumar, M.; Belak, J.; Minich, R.

    2007-03-01

    Experimental results from spall tests on aluminum reveal the presence of a dense dislocation structure in an annulus around a void that grew under the tensile pulse when a shock wave was reflected at the free surface of the specimen. The proposition is that dislocation emission from the void surface under load is a viable mechanism for void growth. To understand void growth in the absence of diffusive effects, the interstitial-loop emission mechanism under tensile hydrostatic stress is investigated. First, the micromechanics of pile-up formation when interstitial loops are emitted from a void under applied macroscopic loading is reviewed. Demand for surface energy expenditure upon void-surface change is taken into consideration. It is demonstrated that in face-centered cubic metals loop emission from voids with a radius of ˜10 nm is indeed energetically possible in the hydrostatic stress environment generated by shock loading. On the other hand, the levels of hydrostatic stress prevalent in common structural applications are not sufficient to drive loops at equilibrium positions above a ˜10 nm void. However, for voids larger than about 100 nm, the energetics of loop emission are easily met as a necessary condition even under the low stress environment prevalent in structural applications.

  1. Loop diuretics are open-channel blockers of the cystic fibrosis transmembrane conductance regulator with distinct kinetics

    PubMed Central

    Ju, Min; Scott-Ward, Toby S; Liu, Jia; Khuituan, Pissared; Li, Hongyu; Cai, Zhiwei; Husbands, Stephen M; Sheppard, David N

    2014-01-01

    BACKGROUND AND PURPOSE Loop diuretics are widely used to inhibit the Na+, K+, 2Cl− co-transporter, but they also inhibit the cystic fibrosis transmembrane conductance regulator (CFTR) Cl− channel. Here, we investigated the mechanism of CFTR inhibition by loop diuretics and explored the effects of chemical structure on channel blockade. EXPERIMENTAL APPROACH Using the patch-clamp technique, we tested the effects of bumetanide, furosemide, piretanide and xipamide on recombinant wild-type human CFTR. KEY RESULTS When added to the intracellular solution, loop diuretics inhibited CFTR Cl− currents with potency approaching that of glibenclamide, a widely used CFTR blocker with some structural similarity to loop diuretics. To begin to study the kinetics of channel blockade, we examined the time dependence of macroscopic current inhibition following a hyperpolarizing voltage step. Like glibenclamide, piretanide blockade of CFTR was time and voltage dependent. By contrast, furosemide blockade was voltage dependent, but time independent. Consistent with these data, furosemide blocked individual CFTR Cl− channels with ‘very fast’ speed and drug-induced blocking events overlapped brief channel closures, whereas piretanide inhibited individual channels with ‘intermediate’ speed and drug-induced blocking events were distinct from channel closures. CONCLUSIONS AND IMPLICATIONS Structure–activity analysis of the loop diuretics suggests that the phenoxy group present in bumetanide and piretanide, but absent in furosemide and xipamide, might account for the different kinetics of channel block by locking loop diuretics within the intracellular vestibule of the CFTR pore. We conclude that loop diuretics are open-channel blockers of CFTR with distinct kinetics, affected by molecular dimensions and lipophilicity. PMID:24117047

  2. Ultrafast electronic disorder in heat-induced structural deformations and phase transitions in metals

    NASA Astrophysics Data System (ADS)

    Guo, Chunlei; Taylor, Antoinette J.

    2000-09-01

    Heat-induced structural deformations and phase transitions of gold and silver are studied using 1.55-eV, 120-fs ultrashort laser pulses. The dynamics of the heating process is monitored by measuring the time evolution of the dielectric constants following optical excitation. Intensity-dependent dielectric constants in silver and gold show similarities with the photon-energy-dependent dielectric constants, which is shown to indirectly map out the degree of heat-induced electronic disorder in these noble metals. This observation strongly suggests that the heat-induced structural deformations and phase transitions in metals are tied to the electronic disorder and band-structure collapse.

  3. Block-copolymer-induced structure formation in microemulsions

    SciTech Connect

    Hilfiker, R.; Eicke, H.F.; Steeb, C.; Hofmeier, U. )

    1991-02-07

    Transient electric birefringence measurements were performed on water/AOT (sodium bis(2-ethylhexyl) sulfosuccinate)/isooctane microemulsions with various amounts of block-copoly(oxyethylene/isoprene/oxyethylene) added. The authors could show that addition of the copolymer leads to a formation of nanodroplet (ND)-copolymer-aggregates. The contributions of NDs and aggregates to the induced birefringence could easily be separated because the NDs exhibited a negative and the aggregates a positive induced birefringence and because the time scales corresponding to the two processes were different.

  4. Radiation-induced apoptosis in the eye structures: a review

    NASA Astrophysics Data System (ADS)

    Belkacémi, Yazid; Huchet, Aymeri; Baudouin, Christophe; Lartigau, Éric

    2005-02-01

    Apoptosis plays a crucial role in tissue homeostasis and in the removal of damaged cells from tissues. Both increased and insufficient cell death can lead to human diseases. Apoptotic process is under the control of physiological metabolism as well as a panel of genes. After exposure to radiation, membrane damages induce the membrane pathway signal transduction for cell apoptosis. The importance of the radiation-induced apoptosis in the different ocular tissues and its relationship to the radiation parameters are reviewed in this article. This topic of ocular research has not been addressed in detail in the literature.

  5. The Anderson Current Loop

    NASA Technical Reports Server (NTRS)

    Anderson, Karl F.

    1994-01-01

    Four-wire-probe concept applied to electrical-resistance transducers. Anderson current loop is excitation-and-signal-conditioning circuit suitable for use with strain gauges, resistance thermometers, and other electrical-resistance transducers mounted in harsh environments. Used as alternative to Wheatstone bridge. Simplifies signal-conditioning problem, enabling precise measurement of small changes in resistance of transducer. Eliminates some uncertainties in Wheatstone-bridge resistance-change measurements in flight research. Current loop configuration makes effects of lead-wire and contact resistances insignificantly small. Also provides output voltage that varies linearly with change in gauge resistance, and does so at double sensitivity of Wheatstone bridge.

  6. Wilson-loop instantons

    NASA Technical Reports Server (NTRS)

    Lee, Kimyeong; Holman, Richard; Kolb, Edward W.

    1987-01-01

    Wilson-loop symmetry breaking is considered on a space-time of the form M4 x K, where M4 is a four-dimensional space-time and K is an internal space with nontrivial and finite fundamental group. It is shown in a simple model that the different vacua obtained by breaking a non-Abelian gauge group by Wilson loops are separated in the space of gauge potentials by a finite energy barrier. An interpolating gauge configuration is then constructed between these vacua and shown to have minimum energy. Finally some implications of this construction are discussed.

  7. Loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Chiou, Dah-Wei

    2015-12-01

    This paper presents an "in-a-nutshell" yet self-contained introductory review on loop quantum gravity (LQG) — a background-independent, nonperturbative approach to a consistent quantum theory of gravity. Instead of rigorous and systematic derivations, it aims to provide a general picture of LQG, placing emphasis on the fundamental ideas and their significance. The canonical formulation of LQG, as the central topic of the paper, is presented in a logically orderly fashion with moderate details, while the spin foam theory, black hole thermodynamics, and loop quantum cosmology are covered briefly. Current directions and open issues are also summarized.

  8. Neuron-like dynamics of a phase-locked loop

    NASA Astrophysics Data System (ADS)

    Matrosov, Valery V.; Mishchenko, Mikhail A.; Shalfeev, Vladimir D.

    2013-10-01

    Dynamics of two coupled phase-controlled generators based on phase-locked loop systems with a high frequency filter in the control loop was studied. It was found that beating modes are synchronized in the systems and shown that different synchronization states form an overlapping structure in parameters space of the coupled systems. Usage of the phase-locked loop as a neuron-like element is proposed.

  9. CREB Selectively Controls Learning-Induced Structural Remodeling of Neurons

    ERIC Educational Resources Information Center

    Middei, Silvia; Spalloni, Alida; Longone, Patrizia; Pittenger, Christopher; O'Mara, Shane M.; Marie, Helene; Ammassari-Teule, Martine

    2012-01-01

    The modulation of synaptic strength associated with learning is post-synaptically regulated by changes in density and shape of dendritic spines. The transcription factor CREB (cAMP response element binding protein) is required for memory formation and in vitro dendritic spine rearrangements, but its role in learning-induced remodeling of neurons…

  10. Flow-induced vibration of circular cylindrical structures

    SciTech Connect

    Chen, S.S.

    1985-06-01

    This report summarizes the flow-induced vibration of circular cylinders in quiescent fluid, axial flow, and crossflow, and applications of the analytical methods and experimental data in design evaluation of various system components consisting of circular cylinders. 219 figs., 30 tabs. (JDB)

  11. Laser-induced structure formation on stretched polymer foils

    SciTech Connect

    Bityurin, Nikita; Arnold, Nikita; Baeuerle, Dieter; Arenholz, Enno

    2007-04-15

    Noncoherent structures that develop during UV laser ablation of stretched semicrystalline polymer foils are a very general phenomenon. A thermodynamic model based on stress relaxation within the modified layer of the polymer surface describes the main features of the observed phenomena, and, in particular, the dependence of the period of structures on laser wavelength, fluence, and number of laser pulses.

  12. Internal structure changes of eyelash induced by eye makeup.

    PubMed

    Fukami, Ken-Ichi; Inoue, Takafumi; Kawai, Tomomitsu; Takeuchi, Akihisa; Uesugi, Kentaro; Suzuki, Yoshio

    2014-01-01

    To investigate how eye makeup affects eyelash structure, internal structure of eyelashes were observed with a scanning X-ray microscopic tomography system using synchrotron radiation light source. Eyelash samples were obtained from 36 Japanese women aged 20-70 years and whose use of eye makeup differed. Reconstructed cross-sectional images showed that the structure of the eyelash closely resembled that of scalp hair. The eyelash structure is changed by use of eye makeup. There was a positive correlation between the frequency of mascara use and the degree of cracking in cuticle. The positive correlation was also found between the frequency of mascara use and the porosity of the cortex. By contrast, the use of eyelash curler did not affect the eyelash structure with statistical significance.

  13. Livermore Compiler Analysis Loop Suite

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizationsmore » and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

  14. Livermore Compiler Analysis Loop Suite

    SciTech Connect

    Hornung, R. D.

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.

  15. Counting primary loops in polymer gels

    PubMed Central

    Zhou, Huaxing; Woo, Jiyeon; Cok, Alexandra M.; Wang, Muzhou; Olsen, Bradley D.; Johnson, Jeremiah A.

    2012-01-01

    Much of our fundamental knowledge related to polymer networks is built on an assumption of ideal end-linked network structure. Real networks invariably possess topological imperfections that negatively affect mechanical properties; modifications of classical network theories have been developed to account for these defects. Despite decades of effort, there are no known experimental protocols for precise quantification of even the simplest topological network imperfections: primary loops. Here we present a simple conceptual framework that enables primary loop quantification in polymeric materials. We apply this framework to measure the fraction of primary loop junctions in trifunctional PEG-based hydrogels. We anticipate that the concepts described here will open new avenues of theoretical and experimental research related to polymer network structure. PMID:23132947

  16. Strain-induced structural instability in FeRh

    NASA Astrophysics Data System (ADS)

    Aschauer, Ulrich; Braddell, Roisin; Brechbühl, Sonia A.; Derlet, Peter M.; Spaldin, Nicola A.

    2016-07-01

    We perform density functional calculations to investigate the structure of the intermetallic alloy FeRh under epitaxial strain. Bulk FeRh exhibits a metamagnetic transition from a low-temperature antiferromagnetic (AFM) phase to a ferromagnetic phase at 350 K, and its strain dependence is of interest for tuning the transition temperature to the room-temperature operating conditions of typical memory devices. We find an unusually strong dependence of the structural energetics on the choice of exchange-correlation functional, with the usual local density approximation yielding the wrong ground-state structure, and generalized gradient (GGA) extensions being in better agreement with the bulk experimental structure. Using the GGA we show the exis