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Sample records for constructing optimal backbone

  1. Constructing optimal backbone segments for joining fixed DNA base pairs.

    PubMed Central

    Mazur, J; Jernigan, R L; Sarai, A

    1996-01-01

    A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the backbone caused by this positioning of the bases. The entire computational unit comprises several nucleotides that are energy-minimized, subject to constraints imposed by the sugar-phosphate backbone segments being anchored to space-fixed base pairs. The minimization schemes are based on two stages, a conjugate gradient method followed by a Newton-Raphson algorithm. Because our purpose is to examine the response, or relaxation, of an artificially stressed backbone, it is essential to be able to obtain, as closely as possible, a lowest minimum energy conformation of the backbone segment in conformational space. For this purpose, an algorithm is developed that leads to the generation of an assembly of many local energy minima. From these sets of local minima, one conformation corresponding to the one with the lowest minimum is then selected and designated to represent the backbone segment at its minimum. The effective electrostatic potential of mean force is expressed in terms of adjustable parameters that incorporate solvent screening action in the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain the best fit of the nearest-neighbor phosphorous atoms in an x-ray structure. PMID:8874023

  2. Constructing backbone network by using tinker algorithm

    NASA Astrophysics Data System (ADS)

    He, Zhiwei; Zhan, Meng; Wang, Jianxiong; Yao, Chenggui

    2017-01-01

    Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. The functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.

  3. The Construction of Metal-Organic Framework with Active Backbones by the Utilization of Reticular Chemistry

    NASA Astrophysics Data System (ADS)

    Choi, Eunwoo

    phenomenon was studied by powder X-ray diffraction and supported by gas adsorption and thermogravimetric analysis. Layered MOFs with metalloporphyrins with Zn, Cu, Co and Fe at their +2 oxidation states as struts were prepared to facilitate non-structural metal sites and tested for hydrogen adsorption and the binding enthalpies. Steep uptakes are indeed observed, but rather due to the optimal interlayer distance of 9 A for dihydrogen, and the binding enthalpies are 6.7 -- 7.6 kJ . mo1-1 which are not ·extraordinary. Although the metals did not seem to play a large role, a trend was observed where the binding enthalpies increase as the metals in the metalloporphyrins go from late to early transition metals. With the concept of conductive metal oxides, a journey of constructing conductive MOFs was taken by attempting the formation of metal-carbon bonds by linking transition metal ions with conjugated organic struts which are 1,4-benzenediisonitrile, 1,4-benzenediethynylide and p-cyanophenylethynylide. Among the attempted systems, a reaction of Cr(III) and 1,4-benzenediethynylide yielded an amorphous material with a BET (Brunauer-Emmett-Teller) surface area of 80 m2.g-1, hydrogen uptake of 47 cm 3. g-1 and a resistance of 20 MO. Also a crystalline compound was prepared by mimicking Prussian blue by using p-cyanophenylethynylide where one end can bind metal with ethynylic carbon and the other end with the cyano nitrogen by following the similar synthesis of Prussian blue analogues. The principles of reticular chemistry are demonstrated through each chapter and show how powerful and beneficial reticular chemistry is by allowing the predetermination of the structure and function. The details of the ways to approach an ideal compound and the synthetic aspects are also described in this dissertation.

  4. Constructing optimal entanglement witnesses

    SciTech Connect

    Chruscinski, Dariusz; Pytel, Justyna; Sarbicki, Gniewomir

    2009-12-15

    We provide a class of indecomposable entanglement witnesses. In 4x4 case, it reproduces the well-known Breuer-Hall witness. We prove that these witnesses are optimal and atomic, i.e., they are able to detect the 'weakest' quantum entanglement encoded into states with positive partial transposition. Equivalently, we provide a construction of indecomposable atomic maps in the algebra of 2kx2k complex matrices. It is shown that their structural physical approximations give rise to entanglement breaking channels. This result supports recent conjecture by Korbicz et al. [Phys. Rev. A 78, 062105 (2008)].

  5. Lightweight mirror construction optimization

    NASA Astrophysics Data System (ADS)

    Mooney, J. T.; Allen, M. A.; Bolton, J.; Dahl, R. J.; Lintz, E. A.

    2015-10-01

    Large, lightweight mirrors are a critical component in space based imaging applications. These mirrors have traditionally required long manufacturing cycle times with associated high costs. In this paper, the key cost and schedule drivers for the production of large, lightweight mirrors will be reviewed along with enabling solutions that could provide significant cost and schedule reductions while maintaining the high quality performance required for these challenging applications. The technologies include advancements in replication, construction, and bonding. Initial feasibility tests and associated results will be presented.

  6. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

    PubMed Central

    2016-01-01

    Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

  7. Optimized Construction of SSR-enriched Libraries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a more efficient method to construct simple sequence repeat (SSR) libraries. We have designed and tested several new adapter. We changed the typical blunt-end ligation of adapters for the more effective sticky-end ligation. We optimized temperature, enzymes and length of each st...

  8. Sequestration of dyes from artificially prepared textile effluent using RSM-CCD optimized hybrid backbone based adsorbent-kinetic and equilibrium studies.

    PubMed

    Sukriti; Sharma, Jitender; Chadha, Amritpal Singh; Pruthi, Vaishali; Anand, Prerna; Bhatia, Jaspreet; Kaith, B S

    2017-04-01

    Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained. Incorporation of polyvinyl alcohol chains onto hybrid backbone and crosslinking between the different polymer chains were confirmed through techniques like FTIR, SEM-EDX and XRD. Semi-IPN was found to be very efficient in the removal of cationic dyes rhodamine-B (70%) and auramine-O (63%) from a mixture with an adsorbent dose of 700 mg, initial concentration of rhodamine-B 6 mgL(-1) and auramine-O 26 mgL(-1), at an time interval of 22-25 h and 30 °C temp. Further to determine the nature of adsorption Langmuir and Freundlich adsorption isotherm models were studied and it was found that Langmuir adsorption isotherm was the best fit model for the removal of mixture of dyes. Kinetic studies for the sorption of dyes favored the reaction mechanism to occur via a pseudo second order pathway with R(2) value about 0.99.

  9. Optimal atlas construction through hierarchical image registration

    NASA Astrophysics Data System (ADS)

    Grevera, George J.; Udupa, Jayaram K.; Odhner, Dewey; Torigian, Drew A.

    2016-03-01

    Atlases (digital or otherwise) are common in medicine. However, there is no standard framework for creating them from medical images. One traditional approach is to pick a representative subject and then proceed to label structures/regions of interest in this image. Another is to create a "mean" or average subject. Atlases may also contain more than a single representative (e.g., the Visible Human contains both a male and a female data set). Other criteria besides gender may be used as well, and the atlas may contain many examples for a given criterion. In this work, we propose that atlases be created in an optimal manner using a well-established graph theoretic approach using a min spanning tree (or more generally, a collection of them). The resulting atlases may contain many examples for a given criterion. In fact, our framework allows for the addition of new subjects to the atlas to allow it to evolve over time. Furthermore, one can apply segmentation methods to the graph (e.g., graph-cut, fuzzy connectedness, or cluster analysis) which allow it to be separated into "sub-atlases" as it evolves. We demonstrate our method by applying it to 50 3D CT data sets of the chest region, and by comparing it to a number of traditional methods using measures such as Mean Squared Difference, Mattes Mutual Information, and Correlation, and for rigid registration. Our results demonstrate that optimal atlases can be constructed in this manner and outperform other methods of construction using freely available software.

  10. An Optimal CDS Construction Algorithm with Activity Scheduling in Ad Hoc Networks.

    PubMed

    Penumalli, Chakradhar; Palanichamy, Yogesh

    2015-01-01

    A new energy efficient optimal Connected Dominating Set (CDS) algorithm with activity scheduling for mobile ad hoc networks (MANETs) is proposed. This algorithm achieves energy efficiency by minimizing the Broadcast Storm Problem [BSP] and at the same time considering the node's remaining energy. The Connected Dominating Set is widely used as a virtual backbone or spine in mobile ad hoc networks [MANETs] or Wireless Sensor Networks [WSN]. The CDS of a graph representing a network has a significant impact on an efficient design of routing protocol in wireless networks. Here the CDS is a distributed algorithm with activity scheduling based on unit disk graph [UDG]. The node's mobility and residual energy (RE) are considered as parameters in the construction of stable optimal energy efficient CDS. The performance is evaluated at various node densities, various transmission ranges, and mobility rates. The theoretical analysis and simulation results of this algorithm are also presented which yield better results.

  11. AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences

    PubMed Central

    Lapidoth, Gideon D.; Baran, Dror; Pszolla, Gabriele M.; Norn, Christoffer; Alon, Assaf; Tyka, Michael D.; Fleishman, Sarel J.

    2016-01-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function – essential to exert control over all polypeptide degrees of freedom – remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in six the backbone conformation at the core of the antibody binding surface is similar to the natural antibody targets, and in several cases sequence and sidechain conformations recapitulate those seen in the natural antibodies. In the case of an anti-lysozyme antibody, designed antibody CDRs at the periphery of the interface, such as L1 and H2, show a greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, which could enhance affinity and specificity. PMID:25670500

  12. Process Model Construction and Optimization Using Statistical Experimental Design,

    DTIC Science & Technology

    1988-04-01

    Memo No. 88-442 ~LECTE March 1988 31988 %,.. MvAY 1 98 0) PROCESS MODEL CONSTRUCTION AND OPTIMIZATION USING STATISTICAL EXPERIMENTAL DESIGN Emmanuel...Sachs and George Prueger Abstract A methodology is presented for the construction of process models by the combination of physically based mechanistic...253-8138. .% I " Process Model Construction and Optimization Using Statistical Experimental Design" by Emanuel Sachs Assistant Professor and George

  13. Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.

    PubMed

    Hefke, Frederik; Bagaria, Anurag; Reckel, Sina; Ullrich, Sandra Johanna; Dötsch, Volker; Glaubitz, Clemens; Güntert, Peter

    2011-02-01

    We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with (13)C or/and (15)N such that cross peaks between (13)CO(i - 1) and (15)NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with (13)C and the second with (15)N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B(2)R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin.

  14. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    PubMed

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.

  15. Constructing DNA Barcode Sets based on Particle Swarm Optimization.

    PubMed

    Waang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi

    2017-03-07

    Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

  16. Optimization of circuits using a constructive learning algorithm

    SciTech Connect

    Beiu, V.

    1997-05-01

    The paper presents an application of a constructive learning algorithm to optimization of circuits. For a given Boolean function f. a fresh constructive learning algorithm builds circuits belonging to the smallest F{sub n,m} class of functions (n inputs and having m groups of ones in their truth table). The constructive proofs, which show how arbitrary Boolean functions can be implemented by this algorithm, are shortly enumerated An interesting aspect is that the algorithm can be used for generating both classical Boolean circuits and threshold gate circuits (i.e. analogue inputs and digital outputs), or a mixture of them, thus taking advantage of mixed analogue/digital technologies. One illustrative example is detailed The size and the area of the different circuits are compared (special cost functions can be used to closer estimate the area and the delay of VLSI implementations). Conclusions and further directions of research are ending the paper.

  17. Construction and preliminary investigation of a novel dengue serotype 4 chimeric virus using Japanese encephalitis vaccine strain SA14-14-2 as the backbone.

    PubMed

    Li, Zhushi; Yang, Huiqiang; Yang, Jian; Lin, Hua; Wang, Wei; Liu, Lina; Zhao, Yu; Liu, Li; Zeng, Xianwu; Yu, Yongxin; Li, Yuhua

    2014-10-13

    For the purpose of developing a novel dengue vaccine candidate, recombinant plasmids were constructed which contained the full length cDNA clone of Japanese encephalitis (JE) vaccine strain SA14-14-2 with its premembrane (PreM) and envelope (E) genes replaced by the counterparts of dengue virus type 4 (DENV4). By transfecting the in vitro transcription products of the recombinant plasmids into BHK-21 cells, a chimeric virus JEV/DENV4 was successfully recovered. The chimeric virus was identified by complete genome sequencing, Western blot and immunofluorescent staining. Growth characteristics revealed it was well adapted to primary hamster kidney (PHK) cells. Its genetic stability was investigated and only one unintentional mutation in 5'-untranslated region (5'-UTR) was found after 20 passages in PHK cells. Neurotropism, neurovirulence and immunogenicity of the chimeric virus were tested in mice. Besides, the influence of JE vaccine pre-immunization on the neutralizing antibody level induced by the chimeric virus was illuminated. To our knowledge, this is the first chimeric virus incorporating the JE vaccine stain SA14-14-2 and DENV4. It is probably a potential candidate to compose a tetravalent dengue chimeric vaccine.

  18. Constructal method to optimize solar thermochemical reactor design

    SciTech Connect

    Tescari, S.; Mazet, N.; Neveu, P.

    2010-09-15

    The objective of this study is the geometrical optimization of a thermochemical reactor, which works simultaneously as solar collector and reactor. The heat (concentrated solar radiation) is supplied on a small peripheral surface and has to be dispersed in the entire reactive volume in order to activate the reaction all over the material. A similarity between this study and the point to volume problem analyzed by the constructal approach (Bejan, 2000) is evident. This approach was successfully applied to several domains, for example for the coupled mass and conductive heat transfer (Azoumah et al., 2004). Focusing on solar reactors, this work aims to apply constructal analysis to coupled conductive and radiative heat transfer. As a first step, the chemical reaction is represented by a uniform heat sink inside the material. The objective is to optimize the reactor geometry in order to maximize its efficiency. By using some hypothesis, a simplified solution is found. A parametric study provides the influence of different technical and operating parameters on the maximal efficiency and on the optimal shape. Different reactor designs (filled cylinder, cavity and honeycomb reactors) are compared, in order to determine the most efficient structure according to the operating conditions. Finally, these results are compared with a CFD model in order to validate the assumptions. (author)

  19. [Optimization of aerobic/anaerobic subsurface flow constructed wetlands].

    PubMed

    Li, Feng-Min; Shan, Shi; Li, Yuan-Yuan; Li, Yang; Wang, Zheng-Yu

    2012-02-01

    Previous studies showed that setting aerobic and anaerobic paragraph segments in the subsurface constructed wetlands (SFCWs) can improve the COD, NH4(+)-N, and TN removal rate, whereas the oxygen enrichment environment which produced by the artificial aeration could restrain the NO3(-)-N and NO2(-)-N removal process, and to a certain extent, inhibit the denitrification in SFCWs Therefore, in this research the structure and technology of SFCW with aerobic and anaerobic paragraph segments were optimized, by using the multi-point water inflow and setting the corresponding section for the extra pollutant removal. Results showed that with the hydraulic load of 0.06 m3 x (m2 x d)(-1), the COD, NH4(+)-N and TN removal efficiencies in the optimized SFCW achieved 91.6%, 100% and 87.7% respectively. COD/N increased to 10 speedily after the inflow supplement. The multi-point water inflow could add carbon sources, and simultaneously maximum utilization of wetland to remove pollutants. The optimized SFCW could achieve the purposes of purification process optimization, and provide theoretical basis and application foundation for improving the total nitrogen removal efficiency.

  20. Optimal deployment of emissions reduction technologies for construction equipment.

    PubMed

    Bari, Muhammad Ehsanul; Zietsman, Josias; Quadrifoglio, Luca; Farzaneh, Mohamadreza

    2011-06-01

    The objective of this research was to develop a multiobjective optimization model to deploy emissions reduction technologies for nonroad construction equipment to reduce emissions in a cost-effective and optimal manner. Given a fleet of construction equipment emitting different pollutants in the nonattainment (NA) and near -nonattainment (NNA) counties of a state and a set of emissions reduction technologies available for installation on equipment to control pollution/emissions, the model assists in determining the mix of technologies to be deployed so that maximum emissions reduction and fuel savings are achieved within a given budget. Three technologies considered for emissions reduction were designated as X, Y, and Z to keep the model formulation general so that it can be applied for any other set of technologies. Two alternative methods of deploying these technologies on a fleet of equipment were investigated with the methods differing in the technology deployment preference in the NA and NNA counties. The model having a weighted objective function containing emissions reduction benefits and fuel-saving benefits was programmed with C++ and ILOG-CPLEX. For demonstration purposes, the model was applied for a selected construction equipment fleet owned by the Texas Department of Transportation, located in NA and NNA counties of Texas, assuming the three emissions reduction technologies X, Y, and Z to represent, respectively, hydrogen enrichment, selective catalytic reduction, and fuel additive technologies. Model solutions were obtained for varying budget amounts to test the sensitivity of emissions reductions and fuel-savings benefits with increasing the budget. Different mixes of technologies producing maximum oxides of nitrogen (NO(x)) reductions and total combined benefits (emissions reductions plus fuel savings) were indicated at different budget ranges. The initial steep portion of the plots for NO(x) reductions and total combined benefits against budgets

  1. 96 Week Follow-Up of HIV-Infected Patients in Rescue with Raltegravir Plus Optimized Backbone Regimens: A Multicentre Italian Experience

    PubMed Central

    Capetti, Amedeo; Landonio, Simona; Meraviglia, Paola; Di Biagio, Antonio; Lo Caputo, Sergio; Sterrantino, Gaetana; Ammassari, Adriana; Menzaghi, Barbara; Franzetti, Marco; De Socio, Giuseppe Vittorio; Pellicanò, Giovanni; Mazzotta, Elena; Soria, Alessandro; Meschiari, Marianna; Trezzi, Michele; Sasset, Lolita; Celesia, Benedetto Maurizio; Zucchi, Patrizia; Melzi, Sara; Ricci, Elena; Rizzardini, Giuliano

    2012-01-01

    Background Long term efficacy of raltegravir (RAL)-including regimens in highly pre-treated HIV-1-infected patients has been demonstrated in registration trials. However, few studies have assessed durability in routine clinical settings. Methods Antiretroviral treatment-experienced patients initiating a RAL-containing salvage regimen were enrolled. Routine clinical and laboratory follow-up was performed at baseline, week 4, 12, and every 12 weeks thereafter. Data were censored at week 96. Results Out of 320 patients enrolled, 292 (91.25%) subjects maintained their initial regimen for 96 weeks; 28 discontinued prematurely for various reasons: death (11), viral failure (8), adverse events (5), loss to follow-up (3), consent withdrawal (1). Eight among these 28 subjects maintained RAL but changed the accompanying drugs. The mean CD4+ T-cell increase at week 96 was 227/mm3; 273 out of 300 patients (91%), who were still receiving RAL at week 96, achieved viral suppression (HIV-1 RNA <50 copies/mL). When analyzing the immuno-virologic outcome according to the number of drugs used in the regimen, 2 (n = 45), 3 (n = 111), 4 (n = 124), or >4 (n = 40), CD4+ T-cell gain was similar across strata: +270, +214, +216, and +240 cells/mm3, respectively, as was the proportion of subjects with undetectable viral load. Laboratory abnormalities (elevation of liver enzymes, total cholesterol and triglycerides) were rare, ranging from 0.9 to 3.1%. The mean 96-week total cholesterol increase was 23.6 mg/dL. Conclusions In a routine clinical setting, a RAL-based regimen allowed most patients in salvage therapy to achieve optimal viral suppression for at least 96 weeks, with relevant immunologic gain and very few adverse events. PMID:22808029

  2. Optimizing the Construction of the A1 Collaboration Neutron Detector

    NASA Astrophysics Data System (ADS)

    Chinn, Edward; A1 Collaboration

    2016-09-01

    We report on the design and construction of a frame designed to optimize both the time efficiency and construction quality of the large scintillator elements These elements will be assembled to form a neutron detector for use by the A1 Collaboration at the Institute for Nuclear Physics in Mainz, Germany. The design had to provide adequate support for the 20 kg scintillator bars while gluing light guides and photomultiplier tubes to both sides of the bars using optical cement. The optical cement requires approximately 24 hours to dry and 100 bars have to be glued with this apparatus. To address each of these issues, several different prototypes were designed and reviewed. The selected apparatus minimized size to meet space constraints, with reduced material cost and provided the most time-efficient way to build the neutron detector. Once the schematic design was selected, we produced technical drawings in AutoDesk Inventor. Assembled the structure and completed gluing of the first batch of scintillators, in order to verify the performance. This apparatus was successful at producing high quality scintillators which were evaluated using cosmic rays. National Science Foundation Grant No. IIA-1358175.

  3. Fluid management in the optimization of space construction

    NASA Technical Reports Server (NTRS)

    Snyder, Howard

    1990-01-01

    Fluid management impacts strongly on the optimization of space construction. Large quantities of liquids are needed for propellants and life support. The mass of propellant liquids is comparable to that required for the structures. There may be a strong dynamic interaction between the stored liquids and the space structure unless the design minimizes the interaction. The constraints of cost and time required optimization of the supply/resupply strategy. The proper selection and design of the fluid management methods for: slosh control; stratification control; acquisition; transfer; gauging; venting; dumping; contamination control; selection of tank configuration and size; the storage state and the control system can improve the entire system performance substantially. Our effort consists of building mathematical/computer models of the various fluid management methods and testing them against the available experimental data. The results of the models are used as inputs to the system operations studies. During the past year, the emphasis has been on modeling: the transfer of cryogens; sloshing and the storage configuration. The work has been intermeshed with ongoing NASA design and development studies to leverage the funds provided by the Center.

  4. Employing Social Network Construction and Analysis in Web Structure Optimization

    NASA Astrophysics Data System (ADS)

    Xagi, Mohamad; Guerbas, Abdelghani; Kianmehr, Keivan; Karampelas, Panagiotis; Ridley, Mick; Alhajj, Reda; Rokne, Jon

    The world wide web is growing continuously and rapidly; it is quickly facilitating the migration of tasks of the daily life into web-based. This trend shows time will come when everyone is forced to use the web for daily activities. Naive users arc the major concern of such a shift; so, it is necessary to have the web ready to serve them. We argue that this requires well optimized websites for users to quickly locate the information they arc looking for. This, on the other hand, becomes more and more important due to the widespread reliance on the many services available on the Internet nowadays. It is true that search engines can facilitate the task of finding the information one is looking for. However, search engines will never replace but do complement the optimization of a website's internal structure based on previously recorded user behavior. In this chapter, wc will present a novel approach for identifying problematic structures in websites. This method consists of two phases. The first phase compares user behavior, derived via web log mining techniques, to a combined analysis of the website's link structure obtained by applying three methods leading to more robust framework and hence strong and consistent outcome: (1) constructing and analyzing a social network of the pages constituting the website by considering both the structure and the usage information; (2) applying the Weighted PageRank algorithm; and (3) applying the Hypertext Induced Topic Selection (HITS) method. In the second phase, we use the term frequency-inverse document frequency (TFIDF) measure to investigate further the correlation between the page that contains the link and the linked to pages in order to further support the findings of the first phase of our approach. We will then show how to use these intermediate results in order to point out problematic website structures to the website owner.

  5. Large-scale measurement and modeling of backbone Internet traffic

    NASA Astrophysics Data System (ADS)

    Roughan, Matthew; Gottlieb, Joel

    2002-07-01

    There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

  6. Automatic Construction and Global Optimization of a Multisentiment Lexicon

    PubMed Central

    Zhang, Zhongqiu; Mo, Yuting; Li, Lianbei

    2016-01-01

    Manual annotation of sentiment lexicons costs too much labor and time, and it is also difficult to get accurate quantification of emotional intensity. Besides, the excessive emphasis on one specific field has greatly limited the applicability of domain sentiment lexicons (Wang et al., 2010). This paper implements statistical training for large-scale Chinese corpus through neural network language model and proposes an automatic method of constructing a multidimensional sentiment lexicon based on constraints of coordinate offset. In order to distinguish the sentiment polarities of those words which may express either positive or negative meanings in different contexts, we further present a sentiment disambiguation algorithm to increase the flexibility of our lexicon. Lastly, we present a global optimization framework that provides a unified way to combine several human-annotated resources for learning our 10-dimensional sentiment lexicon SentiRuc. Experiments show the superior performance of SentiRuc lexicon in category labeling test, intensity labeling test, and sentiment classification tasks. It is worth mentioning that, in intensity label test, SentiRuc outperforms the second place by 21 percent. PMID:28042290

  7. Automatic Construction and Global Optimization of a Multisentiment Lexicon.

    PubMed

    Yang, Xiaoping; Zhang, Zhongxia; Zhang, Zhongqiu; Mo, Yuting; Li, Lianbei; Yu, Li; Zhu, Peican

    2016-01-01

    Manual annotation of sentiment lexicons costs too much labor and time, and it is also difficult to get accurate quantification of emotional intensity. Besides, the excessive emphasis on one specific field has greatly limited the applicability of domain sentiment lexicons (Wang et al., 2010). This paper implements statistical training for large-scale Chinese corpus through neural network language model and proposes an automatic method of constructing a multidimensional sentiment lexicon based on constraints of coordinate offset. In order to distinguish the sentiment polarities of those words which may express either positive or negative meanings in different contexts, we further present a sentiment disambiguation algorithm to increase the flexibility of our lexicon. Lastly, we present a global optimization framework that provides a unified way to combine several human-annotated resources for learning our 10-dimensional sentiment lexicon SentiRuc. Experiments show the superior performance of SentiRuc lexicon in category labeling test, intensity labeling test, and sentiment classification tasks. It is worth mentioning that, in intensity label test, SentiRuc outperforms the second place by 21 percent.

  8. Constructing optimized binary masks for reservoir computing with delay systems

    NASA Astrophysics Data System (ADS)

    Appeltant, Lennert; van der Sande, Guy; Danckaert, Jan; Fischer, Ingo

    2014-01-01

    Reservoir computing is a novel bio-inspired computing method, capable of solving complex tasks in a computationally efficient way. It has recently been successfully implemented using delayed feedback systems, allowing to reduce the hardware complexity of brain-inspired computers drastically. In this approach, the pre-processing procedure relies on the definition of a temporal mask which serves as a scaled time-mutiplexing of the input. Originally, random masks had been chosen, motivated by the random connectivity in reservoirs. This random generation can sometimes fail. Moreover, for hardware implementations random generation is not ideal due to its complexity and the requirement for trial and error. We outline a procedure to reliably construct an optimal mask pattern in terms of multipurpose performance, derived from the concept of maximum length sequences. Not only does this ensure the creation of the shortest possible mask that leads to maximum variability in the reservoir states for the given reservoir, it also allows for an interpretation of the statistical significance of the provided training samples for the task at hand.

  9. ANSS Backbone Station Quality Assessment

    NASA Astrophysics Data System (ADS)

    Leeds, A.; McNamara, D.; Benz, H.; Gee, L.

    2006-12-01

    In this study we assess the ambient noise levels of the broadband seismic stations within the United States Geological Survey's (USGS) Advanced National Seismic System (ANSS) backbone network. The backbone consists of stations operated by the USGS as well as several regional network stations operated by universities. We also assess the improved detection capability of the network due to the installation of 13 additional backbone stations and the upgrade of 26 existing stations funded by the Earthscope initiative. This assessment makes use of probability density functions (PDF) of power spectral densities (PSD) (after McNamara and Buland, 2004) computed by a continuous noise monitoring system developed by the USGS- ANSS and the Incorporated Research Institutions in Seismology (IRIS) Data Management Center (DMC). We compute the median and mode of the PDF distribution and rank the stations relative to the Peterson Low noise model (LNM) (Peterson, 1993) for 11 different period bands. The power of the method lies in the fact that there is no need to screen the data for system transients, earthquakes or general data artifacts since they map into a background probability level. Previous studies have shown that most regional stations, instrumented with short period or extended short period instruments, have a higher noise level in all period bands while stations in the US network have lower noise levels at short periods (0.0625-8.0 seconds), high frequencies (8.0- 0.125Hz). The overall network is evaluated with respect to accomplishing the design goals set for the USArray/ANSS backbone project which were intended to increase broadband performance for the national monitoring network.

  10. The backbone of a city

    NASA Astrophysics Data System (ADS)

    Scellato, S.; Cardillo, A.; Latora, V.; Porta, S.

    2006-03-01

    Recent studies have revealed the importance of centrality measures to analyze various spatial factors affecting human life in cities. Here we show how it is possible to extract the backbone of a city by deriving spanning trees based on edge betweenness and edge information. By using as sample cases the cities of Bologna and San Francisco, we show how the obtained trees are radically different from those based on edge lengths, and allow an extended comprehension of the “skeleton” of most important routes that so much affects pedestrian/vehicular flows, retail commerce vitality, land-use separation, urban crime and collective dynamical behaviours.

  11. Optimism and pessimism in the context of health: bipolar opposites or separate constructs?

    PubMed

    Kubzansky, Laura D; Kubzansky, Philip E; Maselko, Joanna

    2004-08-01

    One difficulty plaguing research on dispositional optimism and health is whether optimism and pessimism are bipolar opposites or constitute distinct constructs. The present study examined the Life Orientation Test to determine whether the two-factor structure is explained by method bias (due to measurement) or substantive differences. The authors compared three measurement models: bipolar, bivariate, and method artifact. Optimism and pessimism emerged as distinct constructs due to substantive differences. The authors also considered the validity of optimism and pessimism, examining their relations with psychological and physical health outcomes. Optimism and pessimism were more similar in relation to psychological health than to other health-related behavior or physical health outcomes. However, a strongly interpretable pattern for the relation of optimism and pessimism to the health outcomes did not emerge. Further research may benefit from considering optimism and pessimism as bivariate and also should consider the conceptual components and behavioral mechanisms specific to each variable.

  12. Constructing optimal entanglement witnesses. II. Witnessing entanglement in 4Nx4N systems

    SciTech Connect

    Chruscinski, Dariusz; Pytel, Justyna

    2010-11-15

    We provide a class of optimal nondecomposable entanglement witnesses for 4Nx4N composite quantum systems or, equivalently, another construction of nondecomposable positive maps in the algebra of 4Nx4N complex matrices. This construction provides natural generalization of the Robertson map. It is shown that their structural physical approximations give rise to entanglement breaking channels.

  13. The Backbone of the Climate Networks

    NASA Astrophysics Data System (ADS)

    Zou, Y.; Donges, J. F.; Marwan, N.; Kurths, J.

    2009-12-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis. Furthermore, we introduce significance tests to quantify the robustness of measured network properties to uncertainties. References: [1] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Complex networks in climate dynamics -- -- Comparing linear and nonlinear network construction methods. European Physical Journal -- Special Topics, 174, 157-179, 2009. [2] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Backbone of the climate network. Europhysics Letters, in press, 2009.

  14. Optimal measurement model is crucial to identify distinct constructs.

    PubMed

    Gandhi, Pranav

    2010-06-01

    This is a Brief Commentary in response to article-"Steinsbekk, S., Jozefiak, T., Ødegård, R., & Wichstrøm, L. (2009). Impaired parent-reported quality of life in treatment-seeking children with obesity is mediated with high levels of psychopathology. Quality of Life Research, 18(9), 1159-1167. doi: 10.1007/s11136-009-9535-6 ." The commentary states that the investigation of the hypothesis if quality of life and psychopathology are two separate constructs may have been hampered by the use of a suboptimal measurement model.

  15. Split Bregman's optimization method for image construction in compressive sensing

    NASA Astrophysics Data System (ADS)

    Skinner, D.; Foo, S.; Meyer-Bäse, A.

    2014-05-01

    The theory of compressive sampling (CS) was reintroduced by Candes, Romberg and Tao, and D. Donoho in 2006. Using a priori knowledge that a signal is sparse, it has been mathematically proven that CS can defY Nyquist sampling theorem. Theoretically, reconstruction of a CS image relies on the minimization and optimization techniques to solve this complex almost NP-complete problem. There are many paths to consider when compressing and reconstructing an image but these methods have remained untested and unclear on natural images, such as underwater sonar images. The goal of this research is to perfectly reconstruct the original sonar image from a sparse signal while maintaining pertinent information, such as mine-like object, in Side-scan sonar (SSS) images. Goldstein and Osher have shown how to use an iterative method to reconstruct the original image through a method called Split Bregman's iteration. This method "decouples" the energies using portions of the energy from both the !1 and !2 norm. Once the energies are split, Bregman iteration is used to solve the unconstrained optimization problem by recursively solving the problems simultaneously. The faster these two steps or energies can be solved then the faster the overall method becomes. While the majority of CS research is still focused on the medical field, this paper will demonstrate the effectiveness of the Split Bregman's methods on sonar images.

  16. New optimal asymmetric quantum codes constructed from constacyclic codes

    NASA Astrophysics Data System (ADS)

    Xu, Gen; Li, Ruihu; Guo, Luobin; Lü, Liangdong

    2017-02-01

    In this paper, we propose the construction of asymmetric quantum codes from two families of constacyclic codes over finite field 𝔽q2 of code length n, where for the first family, q is an odd prime power with the form 4t + 1 (t ≥ 1 is integer) or 4t ‑ 1 (t ≥ 2 is integer) and n1 = q2+1 2; for the second family, q is an odd prime power with the form 10t + 3 or 10t + 7 (t ≥ 0 is integer) and n2 = q2+1 5. As a result, families of new asymmetric quantum codes [[n,k,dz/dx

  17. Combined holographic-mechanical optical tweezers: Construction, optimization, and calibration

    SciTech Connect

    Hanes, Richard D. L.; Jenkins, Matthew C.; Egelhaaf, Stefan U.

    2009-08-15

    A spatial light modulator (SLM) and a pair of galvanometer-mounted mirrors (GMM) were combined into an optical tweezers setup. This provides great flexibility as the SLM creates an array of traps, which can be moved smoothly and quickly with the GMM. To optimize performance, the effect of the incidence angle on the SLM with respect to phase and intensity response was investigated. Although it is common to use the SLM at an incidence angle of 45 deg., smaller angles give a full 2{pi} phase shift and an output intensity which is less dependent on the magnitude of the phase shift. The traps were calibrated using an active oscillatory technique and a passive probability distribution method.

  18. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; St. Clair, Terry L.

    1989-01-01

    Continuing research at Langley Research Center on the synthesis and development of new inexpensive flexible aromatic polyimides as adhesives has resulted in a material identified as LARC-F-SO2 with similarities to polyimidesulfone, PISO2, and other flexible backbone polyimides recently reported by Progar and St. Clair. Also prepared and evaluated was an endcapped version of PISO2. These two polymers were compared with LARC-TPI and LARC-STPI, polyimides research in our laboratory and reported in the literature. The adhesive evaluation, primarily based on lap shear strength (LSS) tests at RT, 177 C and 204 C, involved preparing adhesive tapes, conducting bonding studies and exposing lap shear specimens to 204 C air for up to 1000 hrs and to a 72-hour water boil. The type of adhesive failure as well as the Tg was determined for the fractured specimens. The results indicate that LARC-TPI provides the highest LSSs. LARC-F-SO2, LARC-TPI and LARC-STPI all retain their strengths after thermal exposure for 1000 hrs and PISO2 retains greater than 80 percent of its control strengths. After a 72-hr water boil exposure, most of the four adhesive systems showed reduced strengths for all test temperatures although still retaining a high percentage of their original strength (greater than 60 percent) except for one case. The predominant failure type was cohesive with no significant change in the Tgs.

  19. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; St.clair, Terry L.

    1988-01-01

    Continuing research at Langley Research Center on the synthesis and development of new inexpensive flexible aromatic polyimides as adhesives has resulted in a material identified as LARC-F-SO2 with similarities to polyimidesulfone, PISO2, and other flexible backbone polyimides recently reported by Progar and St. Clair. Also prepared and evaluated was an endcapped version of PISO2. These two polymers were compared with LARC-TPI and LARC-STPI, polyimides research in our laboratory and reported in the literature. The adhesive evaluation, primarily based on lap shear strength (LSS) tests at RT, 177 C and 204 C, involved preparing adhesive tapes, conducting bonding studies and exposing lap shear specimens to 204 C air for up to 1000 hrs and to a 72-hour water boil. The type of adhesive failure as well as the Tg was determined for the fractured specimens. The results indicate that LARC-TPI provides the highest LSSs. LARC-F-SO2, LARC-TPI and LARC-STPI all retain their strengths after thermal exposure for 1000 hrs and PISO2 retains greater than 80 percent of its control strengths. After a 72-hr water boil exposure, most of the four adhesive systems showed reduced strengths for all test temperatures although still retaining a high percentage of their original strength (greater than 60 percent) except for one case. The predominant failure type was cohesive with no significant change in the Tgs.

  20. Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications

    NASA Astrophysics Data System (ADS)

    Paredes, Eduardo

    The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating

  1. External Tank - The Structure Backbone

    NASA Technical Reports Server (NTRS)

    Welzyn, Kenneth; Pilet, Jeffrey C.; Diecidue-Conners, Dawn; Worden, Michelle; Guillot, Michelle

    2011-01-01

    The External Tank forms the structural backbone of the Space Shuttle in the launch configuration. Because the tank flies to orbital velocity with the Space Shuttle Orbiter, minimization of weight is mandatory, to maximize payload performance. Choice of lightweight materials both for structure and thermal conditioning was necessary. The tank is large, and unique manufacturing facilities, tooling, handling, and transportation operations were required. Weld processes and tooling evolved with the design as it matured through several block changes, to reduce weight. Non Destructive Evaluation methods were used to assure integrity of welds and thermal protection system materials. The aluminum-lithium alloy was used near the end of the program and weld processes and weld repair techniques had to be refined. Development and implementation of friction stir welding was a substantial technology development incorporated during the Program. Automated thermal protection system application processes were developed for the majority of the tank surface. Material obsolescence was an issue throughout the 40 year program. The final configuration and tank weight enabled international space station assembly in a high inclination orbit allowing international cooperation with the Russian Federal Space Agency. Numerous process controls were implemented to assure product quality, and innovative proof testing was accomplished prior to delivery. Process controls were implemented to assure cleanliness in the production environment, to control contaminants, and to preclude corrosion. Each tank was accepted via rigorous inspections, including non-destructive evaluation techniques, proof testing, and all systems testing. In the post STS-107 era, the project focused on ascent debris risk reduction. This was accomplished via stringent process controls, post flight assessment using substantially improved imagery, and selective redesigns. These efforts were supported with a number of test programs to

  2. Generalized Lions-Peetre interpolation construction and optimal embedding theorems for Sobolev spaces

    SciTech Connect

    Ovchinnikov, V I

    2014-01-31

    In the paper, a new description of the generalized Lions-Peetre method of means is found, which enables one to evaluate the interpolation orbits of spaces constructed by this method. The list of these spaces includes all Lorentz spaces with functional parameters, Orlicz spaces, and spaces close to them. This leads in turn to new optimal embedding theorems for Sobolev spaces produced using the Lions-Peetre construction in rearrangement invariant spaces. It turns out that the optimal space of the embedding is also a generalized Lions-Peetre space whose parameters are explicitly evaluated. Bibliography: 18 titles.

  3. Teacher's Academic Optimism: The Development and Test of a New Construct

    ERIC Educational Resources Information Center

    Hoy, Anita Woolfolk; Hoy, Wayne K.; Kurz, Nan M.

    2008-01-01

    The objective of this exploratory study of teacher beliefs was twofold: first, to determine whether the construct of academic optimism could be defined and measured as an individual teacher characteristic as it has been at the collective school level, and second, to identify sets of teacher beliefs and practices that were good predictors of…

  4. Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions.

    PubMed

    Matta, Chérif F; Castillo, Norberto; Boyd, Russell J

    2006-01-12

    We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

  5. N-acetyl-L-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding . Backbone and side-chain folding, studied at the DFT level of quantum theory

    NASA Astrophysics Data System (ADS)

    Koo, J. C. P.; Chass, G. A.; Perczel, A.; Farkas, Ö.; Varro, A.; Torday, L. L.; Papp, J. Gy.; Csizmadia, I. G.

    2002-09-01

    In this study, we generated and analyzed the side-chain conformational potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N H{\\cdot}{\\cdot}{\\cdot}O=C) and backbone-side-chain (N H{\\cdot}{\\cdot}{\\cdot}O=C; N H{\\cdot}{\\cdot}{\\cdot}OH) hydrogen bonds were analyzed. The appearance of the notoriously absent \\varepsilon_L backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds.

  6. Construction schedule simulation of a diversion tunnel based on the optimized ventilation time.

    PubMed

    Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao

    2009-06-15

    Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method.

  7. Computational protein design with backbone plasticity

    PubMed Central

    MacDonald, James T.; Freemont, Paul S.

    2016-01-01

    The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

  8. Sub-optimal pit construction in predatory ant lion larvae (Myrmeleon sp.).

    PubMed

    Burgess, Matthew G

    2009-10-07

    The impacts on energy gains of two aspects of ant lion pit architecture were investigated in a natural population of pit-building ant lion larvae (Myrmeleon sp.) in Costa Rica. Field and laboratory settings were used to examine the impacts of circumference and depth of the pit on net energy gain rate. An optimization model predicted a point optimum circumference and angle of depression in an unconstrained system, and positive correlations between body mass, pit circumference, and pit angle of depression in the presence of physiological constraints on both measures. Such a physiological constraint is possible in this system due to a large one-time construction cost. All of these correlations were observed in a lab setting with filtered substrate and no competition; though none were significant in the field. Individuals additionally constructed wider, shallower pits in the field. These results are consistent with an angle of depression that is limited by the angle of repose of the substrate in the field, rather than physiology. These results provided suggestive evidence for sub-optimal pit dimensions in Myrmeleon sp., and for the importance of substrate type in understanding the architecture of natural ant lion pits. The model predicted that the frequency of relocation would not affect the optimal angle of depression, but it would affect the optimal pit circumference to a degree proportional to the square root of the change in the average time an ant lion occupies a single pit. These findings challenge the widely held assumption of adaptive optimality in animal foraging.

  9. Construction and application of particle swarm optimization algorithm for ecological spatial data mining

    NASA Astrophysics Data System (ADS)

    Fu, ZhongLiang; Wan, Bin

    2009-10-01

    The research of the regional ecological environment becomes more important to regional Sustainable Development in order to achieve the harmonious relationship between the person and the nature. The advent of spatial information technologies, such as GIS, GPS and RS, have great enhanced our capabilities to collect and capture spatial data. How to discover potentially useful information and knowledge from massive amounts of spatial data is becoming a crucial project for spatial analysis and spatial decision making. Particle Swarm Optimization has a powerful ability for reasoning and semantic representation, which combined with qualitative analysis and quantitative analysis, with prior knowledge and observed data, and provides an effective way to spatial data mining. This paper focuses on construction and learning a Particle Swarm Optimization model for spatial data mining. Firstly, the theory of spatial data mining is introduced and the characteristics of Particle Swarm Optimization are discussed. A framework and process of spatial data mining is proposed. Then we construct a Particle Swarm Optimization model for spatial data mining with the given dataset. The research area is focused on the distribution of pollution sources in Wuhan City. The experimental results demonstrate the feasibility and practical of the proposed approach to spatial data mining. Finally, draw a conclusion and show further avenues for research. Through the empirical study, it has been proved that Particle Swarm Optimization algorithm is feasible and the conclusion can provide instruction for local environmental planning.

  10. The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures.

    PubMed

    Poltev, Valeri; Anisimov, Victor M; Danilov, Victor I; Garcia, Dolores; Sanchez, Carolina; Deriabina, Alexandra; Gonzalez, Eduardo; Rivas, Francisco; Polteva, Nina

    2014-06-01

    Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na(+)-ions (dDMPs) have demonstrated that the main characteristics of Watson-Crick (WC) right-handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar-phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar-phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr-Pur from Pur-Pyr, and Pur-Pyr from Pyr-Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar-phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z-family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex.

  11. A novel approach to phylogenetic tree construction using stochastic optimization and clustering

    PubMed Central

    Qin, Ling; Chen, Yixin; Pan, Yi; Chen, Ling

    2006-01-01

    Background The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. Results A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. Conclusion Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA. PMID:17217517

  12. Construction and optimization of a quantum analog of the Carnot cycle.

    PubMed

    Xiao, Gaoyang; Gong, Jiangbin

    2015-07-01

    The quantum analog of Carnot cycles in few-particle systems consists of two quantum adiabatic steps and two isothermal steps. This construction is formally justified by use of a minimum work principle. It is then shown, using minimal assumptions of work or heat in nanoscale systems, that the heat-to-work efficiency of such quantum heat engine cycles can be further optimized via two conditions regarding the expectation value of some generalized force operators evaluated at equilibrium states. In general the optimized efficiency is system specific, lower than the Carnot efficiency, and dependent upon both temperatures of the cold and hot reservoirs. Simple computational examples are used to illustrate our theory. The results should be an important guide towards the design of favorable working conditions of a realistic quantum heat engine.

  13. Optimizations on supply and distribution of dissolved oxygen in constructed wetlands: A review.

    PubMed

    Liu, Huaqing; Hu, Zhen; Zhang, Jian; Ngo, Huu Hao; Guo, Wenshan; Liang, Shuang; Fan, Jinlin; Lu, Shaoyong; Wu, Haiming

    2016-08-01

    Dissolved oxygen (DO) is one of the most important factors that can influence pollutants removal in constructed wetlands (CWs). However, problems of insufficient oxygen supply and inappropriate oxygen distribution commonly exist in traditional CWs. Detailed analyses of DO supply and distribution characteristics in different types of CWs were introduced. It can be concluded that atmospheric reaeration (AR) served as the promising point on oxygen intensification. The paper summarized possible optimizations of DO in CWs to improve its decontamination performance. Process (tidal flow, drop aeration, artificial aeration, hybrid systems) and parameter (plant, substrate and operating) optimizations are particularly discussed in detail. Since economic and technical defects are still being cited in current studies, future prospects of oxygen research in CWs terminate this review.

  14. Construction and optimization of a quantum analog of the Carnot cycle

    NASA Astrophysics Data System (ADS)

    Xiao, Gaoyang; Gong, Jiangbin

    2015-07-01

    The quantum analog of Carnot cycles in few-particle systems consists of two quantum adiabatic steps and two isothermal steps. This construction is formally justified by use of a minimum work principle. It is then shown, using minimal assumptions of work or heat in nanoscale systems, that the heat-to-work efficiency of such quantum heat engine cycles can be further optimized via two conditions regarding the expectation value of some generalized force operators evaluated at equilibrium states. In general the optimized efficiency is system specific, lower than the Carnot efficiency, and dependent upon both temperatures of the cold and hot reservoirs. Simple computational examples are used to illustrate our theory. The results should be an important guide towards the design of favorable working conditions of a realistic quantum heat engine.

  15. ANSS Backbone Station Installation and Site Characterization

    NASA Astrophysics Data System (ADS)

    Meremonte, M.; Leeds, A.; Overturf, D.; McMillian, J.; Allen, J.; McNamara, D.

    2004-12-01

    During 2004 several new broadband seismic stations have been deployed as a part of the USGS's Advanced National Seismic System (ANSS) backbone and regional networks. New stations include: ERPA, MNTX, OGLA, AMTX, NATX, KCCO, BMO, MARC, TZTN, LAO, DGMT, REDW, KSU1, MOOW, TPAW, LOHW, RAMW. Permanent station locations were chosen to minimize the local noise conditions by recording continuous data and using a quantitative analysis of the statistical distribution of noise power estimates. For each one-hour segment of continuous data, a power spectral density (PSD) is estimated and smoothed in full octave averages at 1/8 octave intervals. Powers for each 1/8 period interval were then accumulated in one dB power bins. A statistical analysis of power bins yields probability density functions (PDFs) as a function of noise power for each of the octave bands at each station and component. Examination of earthquake signal, artifacts related to station operation and episodic cultural noise in the PDFs allow us to estimate both the overall station quality and the level of earth noise at each potential backbone site. The main function of a seismic network, such as the ANSS, is to provide high quality data for earthquake monitoring, source studies, and Earth structure research. The utility of seismic data is greatly increased when noise levels are reduced. A good quantification and understanding of seismic noise is a first step at reducing noise levels in seismic data and improving overall data quality from the ANSS backbone network.

  16. Construction and parameterization of all static and dynamic H2-optimal state feedback solutions, optimal fixed modes, and fixed decoupling zeros

    NASA Technical Reports Server (NTRS)

    Chen, Ben M.; Saberi, Ali; Sannuti, Peddapullaiah; Shamash, Yacov

    1993-01-01

    This paper considers an H2 optimization problem via state feedback. The class of problems dealt with here are general singular type which have a left invertible transfer matrix function from the control input to the controlled output. This class subsumes the regular H2 optimization problems. The paper constructs and parameterizes all the static and dynamic H2 optimal state feedback solutions. Moreover, all the eigenvalues of an optimal closed-loop system are characterized. All optimal closed-loop systems share a set of eigenvalues which are termed here as the optimal fixed modes. Every H2 optimal controller must assign among the closed-loop eigenvalues the set of optimal fixed modes. This set of optimal fixed modes includes a set of optimal fixed decoupling zeros which shows the minimum absolutely necessary number and locations of pole-zero cancellations present in any H2 optimal design. It is shown that both the sets of optimal fixed modes and optimal fixed decoupling zeros do not vary depending upon whether the static or the dynamic controllers are used.

  17. Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

    PubMed

    Li, Min; Zhang, John Zenghui; Xia, Fei

    2016-04-12

    Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

  18. A web-based Decision Support System for the optimal management of construction and demolition waste.

    PubMed

    Banias, G; Achillas, Ch; Vlachokostas, Ch; Moussiopoulos, N; Papaioannou, I

    2011-12-01

    Wastes from construction activities constitute nowadays the largest by quantity fraction of solid wastes in urban areas. In addition, it is widely accepted that the particular waste stream contains hazardous materials, such as insulating materials, plastic frames of doors, windows, etc. Their uncontrolled disposal result to long-term pollution costs, resource overuse and wasted energy. Within the framework of the DEWAM project, a web-based Decision Support System (DSS) application - namely DeconRCM - has been developed, aiming towards the identification of the optimal construction and demolition waste (CDW) management strategy that minimises end-of-life costs and maximises the recovery of salvaged building materials. This paper addresses both technical and functional structure of the developed web-based application. The web-based DSS provides an accurate estimation of the generated CDW quantities of twenty-one different waste streams (e.g. concrete, bricks, glass, etc.) for four different types of buildings (residential, office, commercial and industrial). With the use of mathematical programming, the DeconRCM provides also the user with the optimal end-of-life management alternative, taking into consideration both economic and environmental criteria. The DSS's capabilities are illustrated through a real world case study of a typical five floor apartment building in Thessaloniki, Greece.

  19. Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

    PubMed

    Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

    2016-08-01

    This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

  20. Towards environmental construct validity in animal models of CNS disorders: optimizing translation of preclinical studies.

    PubMed

    Burrows, Emma L; Hannan, Anthony J

    2013-08-01

    There is an enormous demand for new therapeutic interventions for a range of major disorders. The majority of clinical trials in recent years have been unsuccessful despite highly promising preclinical data. Therefore, an urgent issue confronting both the academic and commercial medical research sectors is how to optimize translation of preclinical studies. The vast majority of preclinical studies are currently performed using laboratory mice and rats. We will discuss the various opportunities for optimization of animal models of CNS disorders. One limitation of current approaches is that most studies are conducted on sedentary, unstimulated animals with unlimited access to food in the home cage, thus leading to metabolic and physiological compromise. Environmental enrichment, which enhances sensory stimulation, cognitive activity and physical exercise, has been demonstrated to induce dramatic effects on brain and behavior in both wild-type and genetically modified rodent models, relative to standard-housed littermate controls. Environmental enrichment also exerts beneficial effects outside the CNS, such as a reduction in excess body fat. We propose that therapeutic interventions which are found to show promise in standard-housed preclinical models should be subsequently tested under conditions of greater environmental enrichment to identify therapeutics which continue to show efficacy in housing contexts of superior 'environmental construct validity'. Other possible approaches to optimize the quality, validity and reporting of preclinical studies in animal models are also discussed.

  1. Optimized single-number quantity for rating the airborne sound insulation of constructions: Living sounds.

    PubMed

    Virjonen, Petra; Hongisto, Valtteri; Oliva, David

    2016-12-01

    ISO 717-1 [(1996). International Organization for Standardization, Geneva, Switzerland] and ASTM 413 [(2010). American Society for Testing and Materials International] define various single-number quantities (SNQs) that are commonly used to rate objectively airborne sound insulation of constructions. Recent psychoacoustic evidence suggests that none of them is appropriate for a wide range of living sound stimuli. The purpose of the study was to develop an alternative compromising SNQ for the frequency range 50-5000 Hz that explains well the annoyance caused by various airborne living sounds transmitted from the neighboring dwelling. Optimal reference spectra for different living sounds were found by mathematical optimization. Experimental data from a psychoacoustic laboratory study [Hongisto, Oliva, and Keränen (2014). Acta Acust. Acust. 100, 848-863] were utilized. The subjects (n = 59) had evaluated the disturbance of living sounds that were electrically filtered to mimic transmission through commonly used wall structures. To find a high-performing reference spectrum for living sounds in general, the optimized reference spectra were averaged over all sound types. The resulting SNQ was called Rw + Copt. The related reference spectrum deviates significantly from the reference spectrum for living activities, C50-5000, below 315 Hz. The suggested SNQ correlates better with the subjective disturbance caused by living sounds than any of the present standardized SNQs of ISO 717-1 or ASTM 413.

  2. Homogeneous Canine Chest Phantom Construction: A Tool for Image Quality Optimization.

    PubMed

    Pavan, Ana Luiza Menegatti; Rosa, Maria Eugênia Dela; Giacomini, Guilherme; Bacchim Neto, Fernando Antonio; Yamashita, Seizo; Vulcano, Luiz Carlos; Duarte, Sergio Barbosa; Miranda, José Ricardo de Arruda; de Pina, Diana Rodrigues

    2016-01-01

    Digital radiographic imaging is increasing in veterinary practice. The use of radiation demands responsibility to maintain high image quality. Low doses are necessary because workers are requested to restrain the animal. Optimizing digital systems is necessary to avoid unnecessary exposure, causing the phenomenon known as dose creep. Homogeneous phantoms are widely used to optimize image quality and dose. We developed an automatic computational methodology to classify and quantify tissues (i.e., lung tissue, adipose tissue, muscle tissue, and bone) in canine chest computed tomography exams. The thickness of each tissue was converted to simulator materials (i.e., Lucite, aluminum, and air). Dogs were separated into groups of 20 animals each according to weight. Mean weights were 6.5 ± 2.0 kg, 15.0 ± 5.0 kg, 32.0 ± 5.5 kg, and 50.0 ± 12.0 kg, for the small, medium, large, and giant groups, respectively. The one-way analysis of variance revealed significant differences in all simulator material thicknesses (p < 0.05) quantified between groups. As a result, four phantoms were constructed for dorsoventral and lateral views. In conclusion, the present methodology allows the development of phantoms of the canine chest and possibly other body regions and/or animals. The proposed phantom is a practical tool that may be employed in future work to optimize veterinary X-ray procedures.

  3. Homogeneous Canine Chest Phantom Construction: A Tool for Image Quality Optimization

    PubMed Central

    2016-01-01

    Digital radiographic imaging is increasing in veterinary practice. The use of radiation demands responsibility to maintain high image quality. Low doses are necessary because workers are requested to restrain the animal. Optimizing digital systems is necessary to avoid unnecessary exposure, causing the phenomenon known as dose creep. Homogeneous phantoms are widely used to optimize image quality and dose. We developed an automatic computational methodology to classify and quantify tissues (i.e., lung tissue, adipose tissue, muscle tissue, and bone) in canine chest computed tomography exams. The thickness of each tissue was converted to simulator materials (i.e., Lucite, aluminum, and air). Dogs were separated into groups of 20 animals each according to weight. Mean weights were 6.5 ± 2.0 kg, 15.0 ± 5.0 kg, 32.0 ± 5.5 kg, and 50.0 ± 12.0 kg, for the small, medium, large, and giant groups, respectively. The one-way analysis of variance revealed significant differences in all simulator material thicknesses (p < 0.05) quantified between groups. As a result, four phantoms were constructed for dorsoventral and lateral views. In conclusion, the present methodology allows the development of phantoms of the canine chest and possibly other body regions and/or animals. The proposed phantom is a practical tool that may be employed in future work to optimize veterinary X-ray procedures. PMID:27101001

  4. Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).

    PubMed

    Subramaniam, Sabareesh; Senes, Alessandro

    2014-11-01

    Side chain optimization is an integral component of many protein modeling applications. In these applications, the conformational freedom of the side chains is often explored using libraries of discrete, frequently occurring conformations. Because side chain optimization can pose a computationally intensive combinatorial problem, the nature of these conformer libraries is important for ensuring efficiency and accuracy in side chain prediction. We have previously developed an innovative method to create a conformer library with enhanced performance. The Energy-based Library (EBL) was obtained by analyzing the energetic interactions between conformers and a large number of natural protein environments from crystal structures. This process guided the selection of conformers with the highest propensity to fit into spaces that should accommodate a side chain. Because the method requires a large crystallographic data-set, the EBL was created in a backbone-independent fashion. However, it is well established that side chain conformation is strongly dependent on the local backbone geometry, and that backbone-dependent libraries are more efficient in side chain optimization. Here we present the backbone-dependent EBL (bEBL), whose conformers are independently sorted for each populated region of Ramachandran space. The resulting library closely mirrors the local backbone-dependent distribution of side chain conformation. Compared to the EBL, we demonstrate that the bEBL uses fewer conformers to produce similar side chain prediction outcomes, thus further improving performance with respect to the already efficient backbone-independent version of the library.

  5. Telephone wire is backbone of security system

    SciTech Connect

    Brede, K.; Rackson, L.T.

    1995-09-01

    Video provides a variety of low-cost, high-quality solutions in today`s security environment. Cost-conscious managers of power generation stations, casinos, prison facilities, military bases and office buildings are considering using regular telephone wire (unshielded twisted pair-UTP) within their existing systems as the backbone of a video to the PC, personal and video-conferencing and training are other areas where phone wire in a building can save money and provide an alternative to coax or fiber for video. More and more, businesses and government agencies are meeting their needs efficiently by using telephone wires for more than just telephones.

  6. Advanced routing in interplanetary backbone network

    NASA Astrophysics Data System (ADS)

    Xu, Ge; Sheng, Min; Wu, Chengke

    2007-11-01

    Interplanetary (IPN) Internet is a communication infrastructure providing communication services for scientific data delivery and navigation services for the explorer spacecrafts and orbiters of the future deep space missions. The interplanetary backbone network has the unique characteristics hence routing through the backbone network present many challenges that are not presented in traditional networks. Some routing algorithms have been proposed, in which, LPDB integrates the shortest path algorithm and the directional broadcast method to guarantee fast and reliable message delivery. Through this mutipath routing strategy, unpredictable link failures is addressed, but additional network overhead is introduced. In this paper, we propose an improvement of the LPDB named ALPDB in which the source could adaptively decide the next-hop nodes according to the link condition, hence reduce the network overhead. We model this algorithm on the network simulation platform of OPNET and compare it with other applicable algorithms in data passing ratio, data delay and network overhead. The result indicates that the ALPDB algorithm could not only guarantee reliable message delivery, but also decrease the cost significantly.

  7. Nonlinear backbone torsional pair correlations in proteins

    NASA Astrophysics Data System (ADS)

    Long, Shiyang; Tian, Pu

    2016-10-01

    Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two and half decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are mainly spatially long-ranged and are dominantly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional motion for correlated BTPs suggested that such nonlinear correlations are mainly associated aharmonic torsional state transitions and in some cases strongly anisotropic local torsional motion of participating torsions, and occur on widely different and relatively longer time scales. In contrast, correlations between backbone torsions in stable α helices and β strands are mainly linear and spatially short-ranged, and are more likely to associate with harmonic local torsional motion. Further analysis revealed that the direct cause of nonlinear contributions are heterogeneous linear correlations. These findings implicate a general search strategy for novel allosteric modulation sites of protein activities.

  8. Nonlinear backbone torsional pair correlations in proteins

    PubMed Central

    Long, Shiyang; Tian, Pu

    2016-01-01

    Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two and half decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are mainly spatially long-ranged and are dominantly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional motion for correlated BTPs suggested that such nonlinear correlations are mainly associated aharmonic torsional state transitions and in some cases strongly anisotropic local torsional motion of participating torsions, and occur on widely different and relatively longer time scales. In contrast, correlations between backbone torsions in stable α helices and β strands are mainly linear and spatially short-ranged, and are more likely to associate with harmonic local torsional motion. Further analysis revealed that the direct cause of nonlinear contributions are heterogeneous linear correlations. These findings implicate a general search strategy for novel allosteric modulation sites of protein activities. PMID:27708342

  9. An Optimal Parallel Algorithm for Constructing a Spanning Tree on Circular Permutation Graphs

    NASA Astrophysics Data System (ADS)

    Honma, Hirotoshi; Honma, Saki; Masuyama, Shigeru

    The spanning tree problem is to find a tree that connects all the vertices of G. This problem has many applications, such as electric power systems, computer network design and circuit analysis. Klein and Stein demonstrated that a spanning tree can be found in O(log n) time with O(n + m) processors on the CRCW PRAM. In general, it is known that more efficient parallel algorithms can be developed by restricting classes of graphs. Circular permutation graphs properly contain the set of permutation graphs as a subclass and are first introduced by Rotem and Urrutia. They provided O(n2.376) time recognition algorithm. Circular permutation graphs and their models find several applications in VLSI layout. In this paper, we propose an optimal parallel algorithm for constructing a spanning tree on circular permutation graphs. It runs in O(log n) time with O(n/ log n) processors on the EREW PRAM.

  10. Design and construction of miniature artificial ecosystem based on dynamic response optimization

    NASA Astrophysics Data System (ADS)

    Hu, Dawei; Liu, Hong; Tong, Ling; Li, Ming; Hu, Enzhu

    The miniature artificial ecosystem (MAES) is a combination of man, silkworm, salad and mi-croalgae to partially regenerate O2 , sanitary water and food, simultaneously dispose CO2 and wastes, therefore it have a fundamental life support function. In order to enhance the safety and reliability of MAES and eliminate the influences of internal variations and external dis-turbances, it was necessary to configure MAES as a closed-loop control system, and it could be considered as a prototype for future bioregenerative life support system. However, MAES is a complex system possessing large numbers of parameters, intricate nonlinearities, time-varying factors as well as uncertainties, hence it is difficult to perfectly design and construct a prototype through merely conducting experiments by trial and error method. Our research presented an effective way to resolve preceding problem by use of dynamic response optimiza-tion. Firstly the mathematical model of MAES with first-order nonlinear ordinary differential equations including parameters was developed based on relevant mechanisms and experimental data, secondly simulation model of MAES was derived on the platform of MatLab/Simulink to perform model validation and further digital simulations, thirdly reference trajectories of de-sired dynamic response of system outputs were specified according to prescribed requirements, and finally optimization for initial values, tuned parameter and independent parameters was carried out using the genetic algorithm, the advanced direct search method along with parallel computing methods through computer simulations. The result showed that all parameters and configurations of MAES were determined after a series of computer experiments, and its tran-sient response performances and steady characteristics closely matched the reference curves. Since the prototype is a physical system that represents the mathematical model with reason-able accuracy, so the process of designing and

  11. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

    SciTech Connect

    Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.

    2015-12-28

    We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.

  12. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

    NASA Astrophysics Data System (ADS)

    Sorella, S.; Devaux, N.; Dagrada, M.; Mazzola, G.; Casula, M.

    2015-12-01

    We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.

  13. Improved design and optimization of subsurface flow constructed wetlands and sand filters

    NASA Astrophysics Data System (ADS)

    Brovelli, A.; Carranza-Díaz, O.; Rossi, L.; Barry, D. A.

    2010-05-01

    Subsurface flow constructed wetlands and sand filters are engineered systems capable of eliminating a wide range of pollutants from wastewater. These devices are easy to operate, flexible and have low maintenance costs. For these reasons, they are particularly suitable for small settlements and isolated farms and their use has substantially increased in the last 15 years. Furthermore, they are also becoming used as a tertiary - polishing - step in traditional treatment plants. Recent work observed that research is however still necessary to understand better the biogeochemical processes occurring in the porous substrate, their mutual interactions and feedbacks, and ultimately to identify the optimal conditions to degrade or remove from the wastewater both traditional and anthropogenic recalcitrant pollutants, such as hydrocarbons, pharmaceuticals, personal care products. Optimal pollutant elimination is achieved if the contact time between microbial biomass and the contaminated water is sufficiently long. The contact time depends on the hydraulic residence time distribution (HRTD) and is controlled by the hydrodynamic properties of the system. Previous reports noted that poor hydrodynamic behaviour is frequent, with water flowing mainly through preferential paths resulting in a broad HRTD. In such systems the flow rate must be decreased to allow a sufficient proportion of the wastewater to experience the minimum residence time. The pollutant removal efficiency can therefore be significantly reduced, potentially leading to the failure of the system. The aim of this work was to analyse the effect of the heterogeneous distribution of the hydraulic properties of the porous substrate on the HRTD and treatment efficiency, and to develop an improved design methodology to reduce the risk of system failure and to optimize existing systems showing poor hydrodynamics. Numerical modelling was used to evaluate the effect of substrate heterogeneity on the breakthrough curves of

  14. Organ sample generator for expected treatment dose construction and adaptive inverse planning optimization

    SciTech Connect

    Nie Xiaobo; Liang Jian; Yan Di

    2012-12-15

    Purpose: To create an organ sample generator (OSG) for expected treatment dose construction and adaptive inverse planning optimization. The OSG generates random samples of organs of interest from a distribution obeying the patient specific organ variation probability density function (PDF) during the course of adaptive radiotherapy. Methods: Principle component analysis (PCA) and a time-varying least-squares regression (LSR) method were used on patient specific geometric variations of organs of interest manifested on multiple daily volumetric images obtained during the treatment course. The construction of the OSG includes the determination of eigenvectors of the organ variation using PCA, and the determination of the corresponding coefficients using time-varying LSR. The coefficients can be either random variables or random functions of the elapsed treatment days depending on the characteristics of organ variation as a stationary or a nonstationary random process. The LSR method with time-varying weighting parameters was applied to the precollected daily volumetric images to determine the function form of the coefficients. Eleven h and n cancer patients with 30 daily cone beam CT images each were included in the evaluation of the OSG. The evaluation was performed using a total of 18 organs of interest, including 15 organs at risk and 3 targets. Results: Geometric variations of organs of interest during h and n cancer radiotherapy can be represented using the first 3 {approx} 4 eigenvectors. These eigenvectors were variable during treatment, and need to be updated using new daily images obtained during the treatment course. The OSG generates random samples of organs of interest from the estimated organ variation PDF of the individual. The accuracy of the estimated PDF can be improved recursively using extra daily image feedback during the treatment course. The average deviations in the estimation of the mean and standard deviation of the organ variation PDF for h

  15. Construction

    DTIC Science & Technology

    2002-01-01

    Harbor Deepening Project, Jacksonville, FL Palm Valley Bridge Project, Jacksonville, FL Rotary Club of San Juan, San Juan, PR Tren Urbano Subway...David. What is nanotechnology? What are its implications for construction?, Foresight/CRISP Workshop on Nanotechnology, Royal Society of Arts

  16. Construction

    DTIC Science & Technology

    2002-01-01

    San Juan, PR Tren Urbano Subway Project, San Juan, PR U.S. Army South, San Juan, PR U.S. Coast Guard Housing Project, San Juan, PR U.S. Coast Guard...construction?, Foresight/CRISP Workshop on Nanotechnology, Royal Society of Arts . Cheltenham, England: 2001, p.5. 56 Concrete Proposals, Economist, July 24

  17. Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

    PubMed Central

    Vision, T J; Brown, D G; Shmoys, D B; Durrett, R T; Tanksley, S D

    2000-01-01

    Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps. PMID:10790413

  18. Construction of a Compact, Low-Inductance, 100 J Dense Plasma Focus for Yield Optimization Studies

    NASA Astrophysics Data System (ADS)

    Cooper, Christopher; Povilus, Alex; Chapman, Steven; Falabella, Steve; Podpaly, Yuri; Shaw, Brian; Liu, Jason; Schmidt, Andrea

    2016-10-01

    A new 100 J mini dense plasma focus (DPF) is constructed to optimize neutron yields for a variety of plasma conditions and anode shapes. The device generates neutrons by leveraging instabilities that occur during a z-pinch in a plasma sheath to accelerate a beam of deuterium ions into a background deuterium gas target. The features that distinguish this miniDPF from previous 100 J devices are a compact, engineered electrode geometry and a low-impedance driver. The driving circuit inductance is minimized by mounting the capacitors close to the back of the anode and cathode < 20 cm away, increasing the breakdown current and yields. The anode can rapidly be changed out to test new designs. The neutron yield and 2D images of the visible light emission are compared to simulations with the hybrid kinetic code LSP which can directly simulate the device and anode designs. Initial studies of the sheath physics and neutron yields for a scaling of discharge voltages and neutral fill pressures are presented. Prepared by LLNL under Contract DE-AC52-07NA27344.

  19. Multi-objective evolutionary optimization for constructing neural networks for virtual reality visual data mining: application to geophysical prospecting.

    PubMed

    Valdés, Julio J; Barton, Alan J

    2007-05-01

    A method for the construction of virtual reality spaces for visual data mining using multi-objective optimization with genetic algorithms on nonlinear discriminant (NDA) neural networks is presented. Two neural network layers (the output and the last hidden) are used for the construction of simultaneous solutions for: (i) a supervised classification of data patterns and (ii) an unsupervised similarity structure preservation between the original data matrix and its image in the new space. A set of spaces are constructed from selected solutions along the Pareto front. This strategy represents a conceptual improvement over spaces computed by single-objective optimization. In addition, genetic programming (in particular gene expression programming) is used for finding analytic representations of the complex mappings generating the spaces (a composition of NDA and orthogonal principal components). The presented approach is domain independent and is illustrated via application to the geophysical prospecting of caves.

  20. Free backbone carbonyls mediate rhodopsin activation

    PubMed Central

    Kimata, Naoki; Pope, Andreyah; Sanchez-Reyes, Omar B.; Eilers, Markus; Opefi, Chikwado A.; Ziliox, Martine; Reeves, Philip J.; Smith, Steven O.

    2016-01-01

    Conserved prolines in the transmembrane helices of G protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilize receptor structure. To address the role of conserved prolines in family A GPCRs, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily, using solid-state NMR spectroscopy. The free backbone C=O groups on helices H5 and H7 are found to stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released facilitating H5 and H7 repacking onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles prolines play in membrane proteins. PMID:27376589

  1. High Speed Fibre Optic Backbone LAN

    NASA Astrophysics Data System (ADS)

    Tanimoto, Masaaki; Hara, Shingo; Kajita, Yuji; Kashu, Fumitoshi; Ikeuchi, Masaru; Hagihara, Satoshi; Tsuzuki, Shinji

    1987-09-01

    Our firm has developed the SUMINET-4100 series, a fibre optic local area network (LAN), to serve the communications system trunk line needs for facilities, such as steel refineries, automobile plants and university campuses, that require large transmission capacity, and for the backbone networks used in intelligent building systems. The SUMINET-4100 series is already in service in various fields of application. Of the networks available in this series, the SUMINET-4150 has a trunk line speed of 128 Mbps and the multiplexer used for time division multiplexing (TDM) was enabled by designing an ECL-TTL gate array (3000 gates) based custom LSI. The synchronous, full-duplex V.24 and V.3.5 interfaces (SUMINET-2100) are provided for use with general purpose lines. And the IBM token ring network, the SUMINET-3200, designed for heterogeneous PCs and the Ethernet can all be connected to sub loops. Further, the IBM 3270 TCA and 5080 CADAM can be connected in the local mode. Interfaces are also provided for the NTT high-speed digital service, the digital PBX systems, and the Video CODEC system. The built-in loop monitor (LM) and network supervisory processor (NSP) provide management of loop utilization and send loop status signals to the host CPU's network configuration and control facility (NCCF). These built-in functions allow both the computer system and LAN to be managed from a single source at the host. This paper outlines features of the SUMINET-4150 and provides an example of its installation.

  2. Detecting the Significant Flux Backbone of Escherichia coli metabolism.

    PubMed

    Güell, Oriol; Sagués, Francesc; Serrano, M Ángeles

    2017-04-09

    The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful for tracing, simultaneously, both its evolution and adaptation fingerprints. This article is protected by copyright. All rights reserved.

  3. Expected treatment dose construction and adaptive inverse planning optimization: Implementation for offline head and neck cancer adaptive radiotherapy

    SciTech Connect

    Yan Di; Liang Jian

    2013-02-15

    Purpose: To construct expected treatment dose for adaptive inverse planning optimization, and evaluate it on head and neck (h and n) cancer adaptive treatment modification. Methods: Adaptive inverse planning engine was developed and integrated in our in-house adaptive treatment control system. The adaptive inverse planning engine includes an expected treatment dose constructed using the daily cone beam (CB) CT images in its objective and constrains. Feasibility of the adaptive inverse planning optimization was evaluated retrospectively using daily CBCT images obtained from the image guided IMRT treatment of 19 h and n cancer patients. Adaptive treatment modification strategies with respect to the time and the number of adaptive inverse planning optimization during the treatment course were evaluated using the cumulative treatment dose in organs of interest constructed using all daily CBCT images. Results: Expected treatment dose was constructed to include both the delivered dose, to date, and the estimated dose for the remaining treatment during the adaptive treatment course. It was used in treatment evaluation, as well as in constructing the objective and constraints for adaptive inverse planning optimization. The optimization engine is feasible to perform planning optimization based on preassigned treatment modification schedule. Compared to the conventional IMRT, the adaptive treatment for h and n cancer illustrated clear dose-volume improvement for all critical normal organs. The dose-volume reductions of right and left parotid glands, spine cord, brain stem and mandible were (17 {+-} 6)%, (14 {+-} 6)%, (11 {+-} 6)%, (12 {+-} 8)%, and (5 {+-} 3)% respectively with the single adaptive modification performed after the second treatment week; (24 {+-} 6)%, (22 {+-} 8)%, (21 {+-} 5)%, (19 {+-} 8)%, and (10 {+-} 6)% with three weekly modifications; and (28 {+-} 5)%, (25 {+-} 9)%, (26 {+-} 5)%, (24 {+-} 8)%, and (15 {+-} 9)% with five weekly modifications. Conclusions

  4. Efficient expression of nattokinase in Bacillus licheniformis: host strain construction and signal peptide optimization.

    PubMed

    Wei, Xuetuan; Zhou, Yinhua; Chen, Jingbang; Cai, Dongbo; Wang, Dan; Qi, Gaofu; Chen, Shouwen

    2015-02-01

    Nattokinase (NK) possesses the potential for prevention and treatment of thrombus-related diseases. In this study, high-level expression of nattokinase was achieved in Bacillus licheniformis WX-02 via host strain construction and signal peptides optimization. First, ten genes (mpr, vpr, aprX, epr, bpr, wprA, aprE, bprA, hag, amyl) encoding for eight extracellular proteases, a flagellin and an amylase were deleted to obtain B. licheniformis BL10, which showed no extracellular proteases activity in gelatin zymography. Second, the gene fragments of P43 promoter, Svpr, nattokinase and TamyL were combined into pHY300PLK to form the expression vector pP43SNT. In BL10 (pP43SNT), the fermentation activity and product activity per unit of biomass of nattokinase reached 14.33 FU/mL and 2,187.71 FU/g respectively, which increased by 39 and 156 % compared to WX-02 (pP43SNT). Last, Svpr was replaced with SsacC and SbprA, and the maximum fermentation activity (33.83 FU/mL) was achieved using SsacC, which was 229 % higher than that of WX-02 (pP43SNT). The maximum NK fermentation activity in this study reaches the commercial production level of solid state fermentation, and this study provides a promising engineered strain for industrial production of nattokinase, as well as a potential platform host for expression of other target proteins.

  5. Identical repeated backbone of the human genome

    PubMed Central

    2010-01-01

    Background Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation. PMID:20096123

  6. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    SciTech Connect

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  7. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    SciTech Connect

    Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

    1998-12-10

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  8. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    SciTech Connect

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely. {copyright} {ital 1998 American Institute of Physics.}

  9. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    NASA Astrophysics Data System (ADS)

    Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

    1998-12-01

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  10. Construction of pore network models for Berea and Fontainebleau sandstones using non-linear programing and optimization techniques

    NASA Astrophysics Data System (ADS)

    Sharqawy, Mostafa H.

    2016-12-01

    Pore network models (PNM) of Berea and Fontainebleau sandstones were constructed using nonlinear programming (NLP) and optimization methods. The constructed PNMs are considered as a digital representation of the rock samples which were based on matching the macroscopic properties of the porous media and used to conduct fluid transport simulations including single and two-phase flow. The PNMs consisted of cubic networks of randomly distributed pores and throats sizes and with various connectivity levels. The networks were optimized such that the upper and lower bounds of the pore sizes are determined using the capillary tube bundle model and the Nelder-Mead method instead of guessing them, which reduces the optimization computational time significantly. An open-source PNM framework was employed to conduct transport and percolation simulations such as invasion percolation and Darcian flow. The PNM model was subsequently used to compute the macroscopic properties; porosity, absolute permeability, specific surface area, breakthrough capillary pressure, and primary drainage curve. The pore networks were optimized to allow for the simulation results of the macroscopic properties to be in excellent agreement with the experimental measurements. This study demonstrates that non-linear programming and optimization methods provide a promising method for pore network modeling when computed tomography imaging may not be readily available.

  11. A backbone lever-arm effect enhances polymer mechanochemistry.

    PubMed

    Klukovich, Hope M; Kouznetsova, Tatiana B; Kean, Zachary S; Lenhardt, Jeremy M; Craig, Stephen L

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

  12. A backbone lever-arm effect enhances polymer mechanochemistry

    NASA Astrophysics Data System (ADS)

    Klukovich, Hope M.; Kouznetsova, Tatiana B.; Kean, Zachary S.; Lenhardt, Jeremy M.; Craig, Stephen L.

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

  13. Comb-type prepolymers consisting of a polyacrylamide backbone and poly(L-lysine) graft chains for multivalent ligands.

    PubMed

    Asayama, S; Maruyama, A; Akaike, T

    1999-01-01

    The comb-type copolymers consisting of a polyacrylamide (PAAm) backbone and poly(L-lysine) (PLL) graft chains have been prepared as the "prepolymer" for designing multivalent ligands. To regulate the length and density of the clusters of primary amino groups, the Nalpha-carboxyanhydride of Nepsilon-carbobenzoxy (CBZ)-L-lysine was first polymerized using p-vinylbenzylamine as an initiator. The resulting poly(CBZ-L-lysine) macromonomer was then radically copolymerized with AAm, followed by the deprotection of amino groups. For the model study, the reactive clusters of primary amino groups were completely converted into anion clusters by the reaction with succinic anhydride. The model multivalent ligands having the biotin label on the PAAm backbone were prepared by the terpolymerization of the macromonomer, AAm, and the biotin derivative having a vinyl group. The enzyme-linked immunosorbent assay showed that the biotin with no spacer on the PAAm backbone was recognized by the avidin-peroxidase conjugate specifically. Therefore, the highly sensitive detection of the interaction between cells and various model multivalent ligands was possible. The selective labeling onto the PAAm backbone revealed that the converted anion clusters of graft chains interacted exclusively with the cell and that the backbone was inert to the interaction with the cell. These results indicate that the various PAAm-graft-PLL comb-type copolymers with the defined length and density of the PLL-grafts are the potential prepolymers to investigate and to optimize the affinity of the multivalent ligands for receptors.

  14. Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

    PubMed

    Grate, Jay W; Mo, Kai-For; Daily, Michael D

    2016-03-14

    Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions.

  15. A method to combine hydrodynamics and constructive design in the optimization of the runner blades of Kaplan turbines

    NASA Astrophysics Data System (ADS)

    Miclosina, C. O.; Balint, D. I.; Campian, C. V.; Frunzaverde, D.; Ion, I.

    2012-11-01

    This paper deals with the optimization of the axial hydraulic turbines of Kaplan type. The optimization of the runner blade is presented systematically from two points of view: hydrodynamic and constructive. Combining these aspects in order to gain a safer operation when unsteady effects occur in the runner of the turbine is attempted. The design and optimization of the runner blade is performed with QTurbo3D software developed at the Center for Research in Hydraulics, Automation and Thermal Processes (CCHAPT) from "Eftimie Murgu" University of Resita, Romania. QTurbo3D software offers possibilities to design the meridian channel of hydraulic turbines design the blades and optimize the runner blade. 3D modeling and motion analysis of the runner blade operating mechanism are accomplished using SolidWorks software. The purpose of motion study is to obtain forces, torques or stresses in the runner blade operating mechanism, necessary to estimate its lifetime. This paper clearly states the importance of combining the hydrodynamics with the structural design in the optimization procedure of the runner of hydraulic turbines.

  16. Construction of a large synthetic human Fab antibody library on yeast cell surface by optimized yeast mating.

    PubMed

    Baek, Du-San; Kim, Yong-Sung

    2014-03-28

    Yeast surface-displayed antibody libraries provide an efficient and quantitative screening resource for given antigens, but suffer from typically modest library sizes owing to low yeast transformation efficiency. Yeast mating is an attractive method for overcoming the limit of yeast transformation to construct a large, combinatorial antibody library, but the optimal conditions have not been reported. Here, we report a large synthetic human Fab (antigen binding fragment) yeast surface-displayed library generated by stepwise optimization of yeast mating conditions. We first constructed HC (heavy chain) and LC (light chain) libraries, where all of the six CDRs (complementarity-determining regions) of the variable domains were diversified mimicking the human germline antibody repertoires by degenerate codons, onto single frameworks of VH3-23 and Vkappa1-16 germline sequences, in two haploid cells of opposite mating types. Yeast mating conditions were optimized in the order of cell density, media pH, and cell growth phase, yielding a mating efficiency of ~58% between the two haploid cells carrying HC and LC libraries. We constructed two combinatorial Fab libraries with CDR-H3 of 9 or 11 residues in length with colony diversities of more than 10(9) by one round of yeast mating between the two haploid HC and LC libraries, with modest diversity sizes of ~10(7). The synthetic human Fab yeast-displayed libraries exhibited relative amino acid compositions in each position of the six CDRs that were very similar to those of the designed repertoires, suggesting that they are a promising source for human Fab antibody screening.

  17. Integrated and Optimized Energy-Efficient Construction Package for a Community of Production Homes in the Mixed-Humid Climate

    SciTech Connect

    Mallay, D.; Wiehagen, J.; Del Bianco, M.

    2014-10-01

    This research high performance home analyzes how a set of advanced technologies can be integrated into a durable and energy-efficient house in the mixed-humid climate while remaining affordable to homeowners. The technical solutions documented in this report are the cornerstone of the builder's entire business model based on delivering high-performance homes on a production basis as a standard product offering to all price segments of the residential market. Home Innovation Research Labs partnered with production builder Nexus EnergyHomes (CZ 4) and they plan to adopt the successful components of the energy solution package for all 55 homes in the community. The research objective was to optimize the builder's energy solution package based on energy performance and construction costs. All of the major construction features, including envelope upgrades, space conditioning system, hot water system, and solar electric system were analyzed.

  18. Life-management strategies of selection, optimization, and compensation: measurement by self-report and construct validity.

    PubMed

    Freund, Alexandra M; Baltes, Paul B

    2002-04-01

    The authors examined the usefulness of a self-report measure for elective selection, loss-based selection. optimization, and compensation (SOC) as strategies of life management. The expected 4-factor solution was obtained in 2 independent samples (N = 218, 14-87 years; N = 181, 18-89 years) exhibiting high retest stability across 4 weeks (r(tt) = .74-82). As expected, middle-aged adults showed higher endorsement of SOC than younger and older adults. Moreover, SOC showed meaningful convergent and divergent associations to other psychological constructs (e.g., thinking styles, NEO) and evinced positive correlations with measures of well-being which were maintained after other personality and motivational constructs were controlled for. Initial evidence on behavioral associations involving SOC obtained in other studies is summarized.

  19. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

    NASA Astrophysics Data System (ADS)

    Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

    2013-05-01

    We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

  20. Padé spectrum decompositions of quantum distribution functions and optimal hierarchical equations of motion construction for quantum open systems.

    PubMed

    Hu, Jie; Luo, Meng; Jiang, Feng; Xu, Rui-Xue; Yan, Yijing

    2011-06-28

    Padé spectrum decomposition is an optimal sum-over-poles expansion scheme of Fermi function and Bose function [J. Hu, R. X. Xu, and Y. J. Yan, J. Chem. Phys. 133, 101106 (2010)]. In this work, we report two additional members to this family, from which the best among all sum-over-poles methods could be chosen for different cases of application. Methods are developed for determining these three Padé spectrum decomposition expansions at machine precision via simple algorithms. We exemplify the applications of present development with optimal construction of hierarchical equations-of-motion formulations for nonperturbative quantum dissipation and quantum transport dynamics. Numerical demonstrations are given for two systems. One is the transient transport current to an interacting quantum-dots system, together with the involved high-order co-tunneling dynamics. Another is the non-Markovian dynamics of a spin-boson system.

  1. Weighting and Aggregation in Composite Indicator Construction: A Multiplicative Optimization Approach

    ERIC Educational Resources Information Center

    Zhou, P.; Ang, B. W.; Zhou, D. Q.

    2010-01-01

    Composite indicators (CIs) have increasingly been accepted as a useful tool for benchmarking, performance comparisons, policy analysis and public communication in many different fields. Several recent studies show that as a data aggregation technique in CI construction the weighted product (WP) method has some desirable properties. However, a…

  2. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  3. Some Approaches Towards Constructing Optimally Efficient Multigrid Solvers for the Inviscid Flow Equations

    NASA Technical Reports Server (NTRS)

    Sidilkover, David

    1997-01-01

    Some important advances took place during the last several years in the development of genuinely multidimensional upwind schemes for the compressible Euler equations. In particular, a robust, high-resolution genuinely multidimensional scheme which can be used for any of the flow regimes computations was constructed. This paper summarizes briefly these developments and outlines the fundamental advantages of this approach.

  4. Blind Optimism: A Cross-Cultural Study of Students' Temporal Constructs and Their Schooling Engagements

    ERIC Educational Resources Information Center

    Rossatto, Cesar Augusto

    2004-01-01

    This article examines students' perceptions and usage of time, their sense of optimism or lack of it, especially related to schooling. Positionality, or perceptions about life and projections of the future, has great impact on students' success in school. How they interpret the past, live in the present and foresee the future is significantly…

  5. Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.

    PubMed

    Zhou, Hui; Vonk, Brenda; Roubos, Johannes A; Bovenberg, Roel A L; Voigt, Christopher A

    2015-12-02

    Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors.

  6. Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor

    PubMed Central

    Zhou, Hui; Vonk, Brenda; Roubos, Johannes A.; Bovenberg, Roel A.L.; Voigt, Christopher A.

    2015-01-01

    Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors. PMID:26519464

  7. Structural dependencies of protein backbone 2JNC' couplings.

    PubMed

    Juranić, Nenad; Dannenberg, J J; Cornilescu, Gabriel; Salvador, Pedro; Atanasova, Elena; Ahn, Hee-Chul; Macura, Slobodan; Markley, John L; Prendergast, Franklyn G

    2008-04-01

    Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone (2)J(NC') couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental (2)J(NC') couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated (2)J(NC') couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from (h3)J(NC') couplings, provides useful insight into the overall energy profile of the protein backbone in solution.

  8. Structural dependencies of protein backbone 2JNC′ couplings

    PubMed Central

    Juranić, Nenad; Dannenberg, J.J.; Cornilescu, Gabriel; Salvador, Pedro; Atanasova, Elena; Ahn, Hee-Chul; Macura, Slobodan; Markley, John L.; Prendergast, Franklyn G.

    2008-01-01

    Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone 2JNC′ couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental 2JNC′ couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated 2JNC′ couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from h3JNC′ couplings, provides useful insight into the overall energy profile of the protein backbone in solution. PMID:18305196

  9. A homotopy approach for combined control-structure optimization - Constructive analysis and numerical examples

    NASA Technical Reports Server (NTRS)

    Scheid, R. E.; Milman, M. H.; Salama, M.; Bruno, R.; Gibson, J. S.

    1990-01-01

    This paper outlines the development of methods for the combined control-structure optimization of physical systems encountered in the technology of large space structures. The objectives of the approach taken in this paper is not to produce the 'best' optimized design, but rather to efficiently produce a family of design options so as to assist in early trade studies, typically before hard design constraints are imposed. The philosophy is that these are candidate designs to be passed on for further considerations, and their function is more to guide the development of the system design rather than to represent the ultimate product. A homotopy approach involving multi-objective functions is developed for this purpose. Analytical and numerical examples are also presented.

  10. Meta-Heuristics in Short Scale Construction: Ant Colony Optimization and Genetic Algorithm

    PubMed Central

    Schroeders, Ulrich; Wilhelm, Oliver; Olaru, Gabriel

    2016-01-01

    The advent of large-scale assessment, but also the more frequent use of longitudinal and multivariate approaches to measurement in psychological, educational, and sociological research, caused an increased demand for psychometrically sound short scales. Shortening scales economizes on valuable administration time, but might result in inadequate measures because reducing an item set could: a) change the internal structure of the measure, b) result in poorer reliability and measurement precision, c) deliver measures that cannot effectively discriminate between persons on the intended ability spectrum, and d) reduce test-criterion relations. Different approaches to abbreviate measures fare differently with respect to the above-mentioned problems. Therefore, we compare the quality and efficiency of three item selection strategies to derive short scales from an existing long version: a Stepwise COnfirmatory Factor Analytical approach (SCOFA) that maximizes factor loadings and two metaheuristics, specifically an Ant Colony Optimization (ACO) with a tailored user-defined optimization function and a Genetic Algorithm (GA) with an unspecific cost-reduction function. SCOFA compiled short versions were highly reliable, but had poor validity. In contrast, both metaheuristics outperformed SCOFA and produced efficient and psychometrically sound short versions (unidimensional, reliable, sensitive, and valid). We discuss under which circumstances ACO and GA produce equivalent results and provide recommendations for conditions in which it is advisable to use a metaheuristic with an unspecific out-of-the-box optimization function. PMID:27893845

  11. Impact of HIV-1 Backbone on Neutralization Sensitivity: Neutralization Profiles of Heterologous Envelope Glycoproteins Expressed in Native Subtype C and CRF01_AE Backbone

    PubMed Central

    Sanders-Buell, Eric; Wesberry, Maggie; Towle, Teresa; Pillis, Devin M.; Molnar, Sebastian; McLinden, Robert; Edmonds, Tara; Hirsch, Ivan; O’Connell, Robert; McCutchan, Francine E.; Montefiori, David C.; Ochsenbauer, Christina; Kappes, John C.; Kim, Jerome H.; Polonis, Victoria R.; Tovanabutra, Sodsai

    2013-01-01

    Standardized assays to assess vaccine and antiviral drug efficacy are critical for the development of protective HIV-1 vaccines and drugs. These immune assays will be advanced by the development of standardized viral stocks, such as HIV-1 infectious molecular clones (IMC), that i) express a reporter gene, ii) are representative of globally diverse subtypes and iii) are engineered to easily exchange envelope (env) genes for expression of sequences of interest. Thus far, a subtype B IMC backbone expressing Renilla luciferase (LucR), and into which the ectodomain of heterologous env coding sequences can be expressed has been successfully developed but as execution of HIV-1 vaccine efficacy trials shifts increasingly to non-subtype B epidemics (Southern African and Southeast Asia), non-subtype B HIV-1 reagents are needed to support vaccine development. Here we describe two IMCs derived from subtypes C and CRF01_AE HIV-1 primary isolates expressing LucR (IMC.LucR) that were engineered to express heterologous gp160 Envs. 18 constructs expressing various subtypes C and CRF01_AE Envs, mostly acute, in subtype-matched and –unmatched HIV backbones were tested for functionality and neutralization sensitivity. Our results suggest a possible effect of non-env HIV-1 genes on the interaction of Env and neutralizing antibodies and highlight the need to generate a library of IMCs representative of the HIV-1 subtype spectrum to be used as standardized neutralization assay reagents for assessing HIV-1 vaccine efficacy. PMID:24312165

  12. Optimization of operating parameters of hybrid vertical down-flow constructed wetland systems for domestic sewerage treatment.

    PubMed

    Huang, Zhujian; Zhang, Xianning; Cui, Lihua; Yu, Guangwei

    2016-09-15

    In this work, three hybrid vertical down-flow constructed wetland (HVDF-CW) systems with different compound substrates were fed with domestic sewage and their pollutants removal performance under different hydraulic loading and step-feeding ratio was investigated. The results showed that the hydraulic loading and step-feeding ratio were two crucial factors determining the removal efficiency of most pollutants, while substrate types only significantly affected the removal of COD and NH4(+)-N. Generally, the lower the hydraulic loading, the better removal efficiency of all contaminants, except for TN. By contrast, the increase of step-feeding ratio would slightly reduce the removal rate of ammonium and TP but obviously promoted the TN removal. Therefore, the optimal operation of this CWs could be achieved with low hydraulic loading combined with 50% of step-feeding ratio when TN removal is the priority, whereas medium or low hydraulic loading without step-feeding would be suitable when TN removal is not taken into consideration. The obtained results in this study can provide us with a guideline for design and optimization of hybrid vertical flow constructed wetland systems to improve the pollutants removal from domestic sewage.

  13. Improving Water Quality in Construction Site Runoff: Optimal Mixing Time and Dose for Flocculating Suspended Sediment with Polyacrylamide

    NASA Astrophysics Data System (ADS)

    Zare, A. H.

    2015-12-01

    Sediment, a major water pollutant, can harm ecosystems and water resources. Sediment in construction site runoff can be controlled through flocculation using anionic, linear polyacrylamide (PAM), but there is little information on optimizing these applications. We conducted laboratory experiments to determine the optimal mixing times for varying concentrations of two types of polyacrylamide, APS 705 and FA 920, which are blends of polymers with a range of molecular weights that are anionic and neutral, respectively. These were selected from a variety of PAMs previously screened for flocculation potential. Soil from three active construction sites in the Piedmont region of North Carolina were used in the testing. A mixing speed of 300 revolutions per minute (RPM), the maximum available for the paddle mixer we used, was the most effective at reducing turbidity with PAM. Turbidity was reduced with increased mixing times up to a point, after which little additional benefit was evident. For all three soils tested, turbidity decreased as mixing time reached 1-2 minutes at polymer doses of 1, 5 and 10 mg L-1, with no substantial reduction with further mixing. At a polymer dose of 0.5 mg L-1, however, turbidity tended to increase beyond 5 minutes of mixing time, possibly because excessive shear forces destroyed sparsely linked floc. For both PAMs, 1 mg L-1 and a mixing time of 2-3 min appeared to be sufficient to achieve the most effective turbidity reduction.

  14. Optimization in differentiable manifolds in order to determine the method of construction of prehistoric wall paintings.

    PubMed

    Arabadjis, Dimitris; Rousopoulos, Panayiotis; Papaodysseus, Constantin; Exarhos, Michalis; Panagopoulos, Michail; Papazoglou-Manioudaki, Lena

    2011-11-01

    In this paper, a general methodology is introduced for the determination of potential prototype curves used for the drawing of prehistoric wall paintings. The approach includes 1) preprocessing of the wall-paintings contours to properly partition them, according to their curvature, 2) choice of prototype curves families, 3) analysis and optimization in 4-manifold for a first estimation of the form of these prototypes, 4) clustering of the contour parts and the prototypes to determine a minimal number of potential guides, and 5) further optimization in 4-manifold, applied to each cluster separately, in order to determine the exact functional form of the potential guides, together with the corresponding drawn contour parts. The methodology introduced simultaneously deals with two problems: 1) the arbitrariness in data-points orientation and 2) the determination of one proper form for a prototype curve that optimally fits the corresponding contour data. Arbitrariness in orientation has been dealt with a novel curvature based error, while the proper forms of curve prototypes have been exhaustively determined by embedding curvature deformations of the prototypes into 4-manifolds. Application of this methodology to celebrated wall paintings excavated at Tyrins, Greece, and the Greek island of Thera manifests that it is highly probable that these wall paintings were drawn by means of geometric guides that correspond to linear spirals and hyperbolae. These geometric forms fit the drawings’ lines with an exceptionally low average error, less than 0.39 mm. Hence, the approach suggests the existence of accurate realizations of complicated geometric entities more than 1,000 years before their axiomatic formulation in the Classical Ages.

  15. a New Methodology for the Construction of Optimized RUNGE-KUTTA-NYSTRÖM Methods

    NASA Astrophysics Data System (ADS)

    Papadopoulos, D. F.; Simos, T. E.

    In this paper, a new Runge-Kutta-Nyström method of fourth algebraic order is developed. The new method has zero phase-lag, zero amplification error and zero first integrals of the previous properties. Numerical results indicate that the new method is very efficient for solving numerically the Schrödinger equation. We note that for the first time in the literature we use the requirement of vanishing the first integrals of phase-lag and amplification error in the construction of efficient methods for the numerical solution of the Schrödinger equation.

  16. Integrated and Optimized Energy-Efficient Construction Package for a Community of Production Homes in the Mixed-Humid Climate

    SciTech Connect

    Mallay, D.; Wiehagen, J.; Del Bianco, M.

    2014-10-01

    Selection and integration of high performance home features are two sides of the same coin in energy efficient sustainable construction. Many advanced technologies are available for selection, but it is in the integration of these technologies into an affordable set of features that can be used on a production basis by builders, that ensures whole-house performance meets expectations. This research high performance home analyzes how a set of advanced technologies can be integrated into a durable and energy efficient house in the mixed-humid climate while remaining affordable to homeowners. The technical solutions documented in this report are the cornerstone of the builder's entire business model based on delivering high-performance homes on a production basis as a standard product offering to all price segments of the residential market. Home Innovation Research Labs partnered with production builder Nexus EnergyHomes (CZ 4). The builder plans to adopt the successful components of the energy solution package for all 55 homes in the community. The research objective was to optimize the builder's energy solution package based on energy performance and construction costs. All of the major construction features, including envelope upgrades, space conditioning system, hot water system, and solar electric system were analyzed. The information in this report can be used by builders and designers to evaluate options, and the integration of options, for increasing the efficiency of home designs in climate zone 4. The data also provide a point of reference for evaluating estimates of energy savings and costs for specific features.

  17. Mesh optimization for microbial fuel cell cathodes constructed around stainless steel mesh current collectors

    NASA Astrophysics Data System (ADS)

    Zhang, Fang; Merrill, Matthew D.; Tokash, Justin C.; Saito, Tomonori; Cheng, Shaoan; Hickner, Michael A.; Logan, Bruce E.

    Mesh current collectors made of stainless steel (SS) can be integrated into microbial fuel cell (MFC) cathodes constructed of a reactive carbon black and Pt catalyst mixture and a poly(dimethylsiloxane) (PDMS) diffusion layer. It is shown here that the mesh properties of these cathodes can significantly affect performance. Cathodes made from the coarsest mesh (30-mesh) achieved the highest maximum power of 1616 ± 25 mW m -2 (normalized to cathode projected surface area; 47.1 ± 0.7 W m -3 based on liquid volume), while the finest mesh (120-mesh) had the lowest power density (599 ± 57 mW m -2). Electrochemical impedance spectroscopy showed that charge transfer and diffusion resistances decreased with increasing mesh opening size. In MFC tests, the cathode performance was primarily limited by reaction kinetics, and not mass transfer. Oxygen permeability increased with mesh opening size, accounting for the decreased diffusion resistance. At higher current densities, diffusion became a limiting factor, especially for fine mesh with low oxygen transfer coefficients. These results demonstrate the critical nature of the mesh size used for constructing MFC cathodes.

  18. The Graphical Representation of the Digital Astronaut Physiology Backbone

    NASA Technical Reports Server (NTRS)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  19. Backbone fractal dimension and fractal hybrid orbital of protein structure

    NASA Astrophysics Data System (ADS)

    Peng, Xin; Qi, Wei; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2013-12-01

    Fractal geometry analysis provides a useful and desirable tool to characterize the configuration and structure of proteins. In this paper we examined the fractal properties of 750 folded proteins from four different structural classes, namely (1) the α-class (dominated by α-helices), (2) the β-class (dominated by β-pleated sheets), (3) the (α/β)-class (α-helices and β-sheets alternately mixed) and (4) the (α + β)-class (α-helices and β-sheets largely segregated) by using two fractal dimension methods, i.e. "the local fractal dimension" and "the backbone fractal dimension" (a new and useful quantitative parameter). The results showed that the protein molecules exhibit a fractal behavior in the range of 1 ⩽ N ⩽ 15 (N is the number of the interval between two adjacent amino acid residues), and the value of backbone fractal dimension is distinctly greater than that of local fractal dimension for the same protein. The average value of two fractal dimensions decreased in order of α > α/β > α + β > β. Moreover, the mathematical formula for the hybrid orbital model of protein based on the concept of backbone fractal dimension is in good coincidence with that of the similarity dimension. So it is a very accurate and simple method to analyze the hybrid orbital model of protein by using the backbone fractal dimension.

  20. Choice and optimization of ratio of components to develop fast-mounted thermostable heat-insulating constructions

    NASA Astrophysics Data System (ADS)

    Loginova, N. A.; Grigor'ev, S. V.; Lapin, E. E.; Pogorelov, S. I.; Ryzhenkov, A. V.

    2016-05-01

    Fast-mounted heat-insulating constructions based on foamed synthetic rubbers, polyethylene, and polyurethane are characterized by a thermostability up to 150°C and emit toxic substances when burnt. However, there is a need for heat insulation of surfaces with higher coolant temperatures, such as pipelines, equipment of nuclear and thermal power plants, and heating systems with remote heat sources. One of the most promising types of heat insulation materials for creation of fast-mounted heat insulation constructions is the syntactic foams or thin-film multilayer heat-insulating coatings (TFMHIC), which are created using hollow microspheres and various types of binders. The formation of TFMHIC on the heat-insulating surface is carried out mostly by means of spraying methods that have well proven themselves at coating on flat and cylindrical surfaces of large area, but they turned out ineffective for cylindrical surfaces with a diameter of 300 mm and less, since they are characterized by a large degree of carryover of composite material. This article analyzed the binders and microspheres promising to create the fast-mounted heat-insulating constructions based on TFMHIC with high thermostability. Based on the analysis, a conclusion is drawn that organicsilicon binding and glass microspheres are promising for use in the heat-insulating constructions with thermostability up to 300°C. The results of experimental research are given that point to the possibility of predicting the optimal composition of heat-insulating material characterized by a high degree of filling with microspheres with maintaining the mechanical strength, by means of performing the analysis of rheological characteristics of nonpolymerized liquid compositions of heat-insulation material. The index of tensile strength in bending was the criterion for evaluating the mechanical strength of heat-insulating material. The critical volume concentrations of filling the heat-insulating material with glass

  1. Optimal conditions for chlorothalonil and dissolved organic carbon in horizontal subsurface flow constructed wetlands.

    PubMed

    Rìos-Montes, Karina A; Casas-Zapata, Juan C; Briones-Gallardo, Roberto; Peñuela, Gustavo

    2017-01-13

    The most efficient system of horizontal subsurface flow constructed wetlands (HSSFCW) for removing dissolved organic carbon (DOC) in the presence of chlorothalonil pesticide (CLT) present in synthetic domestic wastewater was determined using the macrophyte Phragmites australis. Two concentrations of CLT (85 and 385 μg L(-1)) and one concentration of glucose (20 mg L(-1)) were evaluated in four pilot scale horizontal surface flow constructed wetlands coupled with two sizes of silica gravel, igneous gravel, fine chalky gravel (3.18-6.35 mm), coarse gravel (12.70-25.40 mm) and two water surface heights (20 and 40 cm). For a month, wetlands were acclimated with domestic wastewater. Some groups of bacteria were also identified in the biofilm attached to the gravel. In each treatment periodic samplings were conducted in the influent and effluent. Chlorothalonil was quantified by gas chromatography (GC-ECD m), DOC by an organic carbon analyzer and bacterial groups using conventional microbiology in accordance with Standard Methods. The largest removals of DOC (85.82%-85.31%) were found when using fine gravel (3.18-6.35 mm) and the lower layer of water (20 cm). The bacterial groups quantified in the biofilm were total heterotrophic, revivable heterotrophic, Pseudomonas and total coliforms. The results of this study indicate that fine grain gravel (3.18-6.35 mm) and both water levels (20 to 40 cm) can be used in the removal of organic matter and for the treatment of agricultural effluents contaminated with organo-chloride pesticides like CLT in HSSFCW.

  2. [Construction of optimal combined chemotherapy of anti-tumor drugs based on chronotherapy].

    PubMed

    To, Hideto

    2006-06-01

    Metastatic breast cancer (MBC) is almost always incurable, and the median survival is of the order on 18-24 months. Combination therapy with adriamycin (ADR) and docetaxel (DOC) is more effective against MBC than the previous therapy due to differences between their mechanisms. However, the combination of ADR and DOC induces severe adverse effects, limiting its clinical use in many patients with MBC. The biologic functions of most living organisms are organized along an approximate 24 h time cycle or circadian rhythm. Chronotherapy is defined as the administration of medications using biological rhythms to optimize the therapeutic outcomes and/or control adverse effects. To decrease adverse effects, many antitumor drugs have been particularly studied in humans and animals. The toxicities of ADR and DOC have also been found to depend on dosing-time in animals and humans. This study was to establish the most suitable dosing schedule to relieve severe adverse effects and improve antitumor effects by considering a chronopharmacological approach, dosing-interval and dosing-sequence to the combination chemotherapy of ADR and DOC in mice. In the results, we demonstrate that the dosing schedule based on dosing-sequence, dosing-interval and dosing-time not only significantly reduced leukopenia and toxic death but also significantly increased the inhibition rate of tumor growth compared with the dosing schedule without an interval between each injection, commonly used in clinical practice. These findings suggest that the therapeutic index of combined chemotherapy can be improved by choosing an optimal dosing-schedule (dosing-interval, dosing-sequence and dosing-time).

  3. Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

    NASA Astrophysics Data System (ADS)

    Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

    2015-11-01

    Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex

  4. Optimization of performance assessment and design characteristics in constructed wetlands for the removal of organic matter.

    PubMed

    Hijosa-Valsero, María; Sidrach-Cardona, Ricardo; Martín-Villacorta, Javier; Bécares, Eloy

    2010-10-01

    Some of the most used constructed wetland (CW) configurations [conventional and modified free-water (FW) flow, surface flow, conventional horizontal subsurface flow (SSF) and soilless systems with floating macrophytes (FM)] were assessed in order to compare their efficiencies for the removal of organic pollutants [COD, filtered COD (FCOD), BOD and total suspended solids (TSS)] from urban sewage under the same climatic and wastewater conditions. The removal performance was calculated using three approaches: effluent concentrations, areal removed loads and mass removal. Results were very different depending on the approach, which indicates that the way to present CW efficiency should be considered carefully. All CW-configurations obtained BOD effluent concentrations below 25 mg L(-1) in summer, with a FW-CW with effluent leaving through the bottom of the tank being the only one maintaining low BOD effluent concentrations even in winter and under high organic loading conditions. In this kind of CW, the presence of plants favoured pollutant removal. SSF-CWs were the most efficient for the removal of COD. FM systems can be as efficient as some gravel bed CWs. Typhaangustifolia worked better than Phragmitesaustralis, at least when the systems were at the beginning of their operation period.

  5. Design, construction, and optimization of a novel, modular, and scalable incubation chamber for continuous viral inactivation.

    PubMed

    Orozco, Raquel; Godfrey, Scott; Coffman, Jon; Amarikwa, Linus; Parker, Stephanie; Hernandez, Lindsay; Wachuku, Chinenye; Mai, Ben; Song, Brian; Hoskatti, Shashidhar; Asong, Jinkeng; Shamlou, Parviz; Bardliving, Cameron; Fiadeiro, Marcus

    2017-02-11

    We designed, built or 3D printed, and screened tubular reactors that minimize axial dispersion to serve as incubation chambers for continuous virus inactivation of biological products. Empirical residence time distribution data were used to derive each tubular design's volume equivalent to a theoretical plate (VETP) values at a various process flow rates. One design, the Jig in a Box (JIB), yielded the lowest VETP, indicating optimal radial mixing and minimal axial dispersion. A minimum residence time (MRT) approach was employed, where the MRT is the minimum time the product spends in the tubular reactor. This incubation time is typically 60 minutes in a batch process. We provide recommendations for combinations of flow rates and device dimensions for operation of the JIB connected in series that will meet a 60-min MRT. The results show that under a wide range of flow rates and corresponding volumes, it takes 75 ± 3 min for 99% of the product to exit the reactor while meeting the 60-min MRT criterion and fulfilling the constraint of keeping a differential pressure drop under 5 psi. Under these conditions, the VETP increases slightly from 3 to 5 mL though the number of theoretical plates stays constant at about 1326 ± 88. We also demonstrated that the final design volume was only 6% ± 1% larger than the ideal plug flow volume. Using such a device would enable continuous viral inactivation in a truly continuous process or in the effluent of a batch chromatography column. Viral inactivation studies would be required to validate such a design. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 2017.

  6. Construction and optimization of an efficient amplification method of a random ssDNA library by asymmetric emulsion PCR.

    PubMed

    Shao, Keke; Shi, Xinhui; Zhu, Xiangjun; Cui, Leilei; Shao, Qixiang; Ma, Da

    2015-12-16

    Construction of a random ssDNA sublibrary is an important step of the aptamer screening process. The available construction methods include asymmetric PCR, biotin-streptavidin separation, and lambda exonuclease digestions, in which PCR amplification is a key step. The main drawback of PCR amplification is overamplification increasing nonspecific hybridization among different products and by-products, which may cause the loss of potential high-quality aptamers, inefficient screening, and even screening failure. Cycle number optimization in PCR amplification is the main way to avoid overamplification but does not fundamentally eliminate the nonspecific hybridization, and the decreased cycle number may lead to insufficient product amounts. Here, we developed a new method, "asymmetric emulsion PCR," which could overcome the shortcomings of conventional PCR. In asymmetric emulsion PCR, different templates were separated by emulsion particles, allowing single-molecule PCR, in which each template was separately amplified, and the nonspecific hybridization was avoided. Overamplification or formation of by-products was not observed. The method is so simple that direct amplification of 40 or more cycles can provide a high-quality ssDNA library. Therefore, the asymmetric emulsion PCR would improve the screening efficiency of systematic evolution of ligands by exponential enrichment.

  7. Construction of a directed hammerhead ribozyme library: towards the identification of optimal target sites for antisense-mediated gene inhibition.

    PubMed Central

    Pierce, M L; Ruffner, D E

    1998-01-01

    Antisense-mediated gene inhibition uses short complementary DNA or RNA oligonucleotides to block expression of any mRNA of interest. A key parameter in the success or failure of an antisense therapy is the identification of a suitable target site on the chosen mRNA. Ultimately, the accessibility of the target to the antisense agent determines target suitability. Since accessibility is a function of many complex factors, it is currently beyond our ability to predict. Consequently, identification of the most effective target(s) requires examination of every site. Towards this goal, we describe a method to construct directed ribozyme libraries against any chosen mRNA. The library contains nearly equal amounts of ribozymes targeting every site on the chosen transcript and the library only contains ribozymes capable of binding to that transcript. Expression of the ribozyme library in cultured cells should allow identification of optimal target sites under natural conditions, subject to the complexities of a fully functional cell. Optimal target sites identified in this manner should be the most effective sites for therapeutic intervention. PMID:9801305

  8. Constructing optimal ensemble projections for predictive environmental modelling in Northern Eurasia

    NASA Astrophysics Data System (ADS)

    Anisimov, Oleg; Kokorev, Vasily

    2013-04-01

    Large uncertainties in climate impact modelling are associated with the forcing climate data. This study is targeted at the evaluation of the quality of GCM-based climatic projections in the specific context of predictive environmental modelling in Northern Eurasia. To accomplish this task, we used the output from 36 CMIP5 GCMs from the IPCC AR-5 data base for the control period 1975-2005 and calculated several climatic characteristics and indexes that are most often used in the impact models, i.e. the summer warmth index, duration of the vegetation growth period, precipitation sums, dryness index, thawing degree-day sums, and the annual temperature amplitude. We used data from 744 weather stations in Russia and neighbouring countries to analyze the spatial patterns of modern climatic change and to delineate 17 large regions with coherent temperature changes in the past few decades. GSM results and observational data were averaged over the coherent regions and compared with each other. Ultimately, we evaluated the skills of individual models, ranked them in the context of regional impact modelling and identified top-end GCMs that "better than average" reproduce modern regional changes of the selected meteorological parameters and climatic indexes. Selected top-end GCMs were used to compose several ensembles, each combining results from the different number of models. Ensembles were ranked using the same algorithm and outliers eliminated. We then used data from top-end ensembles for the 2000-2100 period to construct the climatic projections that are likely to be "better than average" in predicting climatic parameters that govern the state of environment in Northern Eurasia. The ultimate conclusions of our study are the following. • High-end GCMs that demonstrate excellent skills in conventional atmospheric model intercomparison experiments are not necessarily the best in replicating climatic characteristics that govern the state of environment in Northern Eurasia

  9. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

    PubMed

    Smith, Colin A; Kortemme, Tanja

    2011-01-01

    Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

  10. Optimized and enhanced DNA plasmid vector based in vivo construction of a neutralizing anti-HIV-1 envelope glycoprotein Fab.

    PubMed

    Muthumani, Kar; Flingai, Seleeke; Wise, Megan; Tingey, Colleen; Ugen, Kenneth E; Weiner, David B

    2013-10-01

    Monoclonal antibody preparations have demonstrated considerable clinical utility in the treatment of specific malignancies, as well as inflammatory and infectious diseases. Antibodies are conventionally delivered by passive administration, typically requiring costly large-scale laboratory development and production. Additional limitations include the necessity for repeat administrations, and the length of in vivo potency. Therefore, the development of methods to generate therapeutic antibodies and antibody like molecules in vivo, distinct from an active antigen-based immunization strategy, would have considerable clinical utility. In fact, adeno-associated viral (AAV) vector mediated delivery of immunoglobulin genes with subsequent generation of functional antibodies has recently been developed. As well, anon-viral vector mediated nucleic acid based delivery technology could permit the generation of therapeutic/prophylactic antibodies in vivo, obviating potential safety issues associated with viral vector based gene delivery. This delivery strategy has limitations as well, mainly due to very low in vivo production and expression of protein from the delivered gene. In the study reported here we have constructed an "enhanced and optimized" DNA plasmid technology to generate immunoglobulin heavy and light chains (i.e., Fab fragments) from an established neutralizing anti-HIV envelope glycoprotein monoclonal antibody (VRC01). This "enhanced" DNA (E-DNA) plasmid technology includes codon/RNA optimization, leader sequence utilization, as well as targeted potentiation of delivery and expression of the Fab immunoglobulin genes through use of "adaptive" in vivo electroporation. The results demonstrate that delivery by this method of a single administration of the optimized Fab expressing constructs resulted in generation of Fab molecules in mouse sera possessing high antigen specific binding and HIV neutralization activity for at least 7 d after injection, against diverse

  11. Identification of systems containing nonlinear stiffnesses using backbone curves

    NASA Astrophysics Data System (ADS)

    Londoño, Julián M.; Cooper, Jonathan E.; Neild, Simon A.

    2017-02-01

    This paper presents a method for the dynamic identification of structures containing discrete nonlinear stiffnesses. The approach requires the structure to be excited at a single resonant frequency, enabling measurements to be made in regimes of large displacements where nonlinearities are more likely to be significant. Measured resonant decay data is used to estimate the system backbone curves. Linear natural frequencies and nonlinear parameters are identified using these backbone curves assuming a form for the nonlinear behaviour. Numerical and experimental examples, inspired by an aerospace industry test case study, are considered to illustrate how the method can be applied. Results from these models demonstrate that the method can successfully deliver nonlinear models able to predict the response of the test structure nonlinear dynamics.

  12. A Pipeline for Constructing Optimized N-Body Models of Interacting Galaxies

    NASA Astrophysics Data System (ADS)

    Harvey, Allen S., Jr.

    friction and determines initial conditions to use for evolution of in an N-Body simulation. These initial conditions are used to create, scale, and reposition unit galaxy models for use in an N-Body simulation of the users choice, and creates the necessary input deck for it. For each simulation, a scoring metric is calculated to determine the quality of fit that the N-Body simulation has in regards to the original SPAM simulation. The scores from each simulation are used in a second order Newton-Raphson optimization step to iterate on values of dynamical friction. This dissertation demonstrates the use of the pipeline to model 54 pairs of interacting galaxies. These models in most cases greatly improve upon the accuracy of faster running models in identifying a set of parameters to define each interacting galaxy with relatively small computational investment. The resulting parameters can be used by higher resolution simulations with more complete sets of physics, such as gas dynamics and star formation, to more readily compare to observational data.

  13. Optimism

    PubMed Central

    Carver, Charles S.; Scheier, Michael F.; Segerstrom, Suzanne C.

    2010-01-01

    Optimism is an individual difference variable that reflects the extent to which people hold generalized favorable expectancies for their future. Higher levels of optimism have been related prospectively to better subjective well-being in times of adversity or difficulty (i.e., controlling for previous well-being). Consistent with such findings, optimism has been linked to higher levels of engagement coping and lower levels of avoidance, or disengagement, coping. There is evidence that optimism is associated with taking proactive steps to protect one's health, whereas pessimism is associated with health-damaging behaviors. Consistent with such findings, optimism is also related to indicators of better physical health. The energetic, task-focused approach that optimists take to goals also relates to benefits in the socioeconomic world. Some evidence suggests that optimism relates to more persistence in educational efforts and to higher later income. Optimists also appear to fare better than pessimists in relationships. Although there are instances in which optimism fails to convey an advantage, and instances in which it may convey a disadvantage, those instances are relatively rare. In sum, the behavioral patterns of optimists appear to provide models of living for others to learn from. PMID:20170998

  14. Geometry motivated alternative view on local protein backbone structures.

    PubMed

    Zacharias, Jan; Knapp, Ernst Walter

    2013-11-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot.

  15. Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

    NASA Technical Reports Server (NTRS)

    Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

    2008-01-01

    Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

  16. RNA-Redesign: a web server for fixed-backbone 3D design of RNA.

    PubMed

    Yesselman, Joseph D; Das, Rhiju

    2015-07-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment.

  17. Retrieving Backbone String Neighbors Provides Insights Into Structural Modeling of Membrane Proteins*

    PubMed Central

    Sun, Jiang-Ming; Li, Tong-Hua; Cong, Pei-Sheng; Tang, Sheng-Nan; Xiong, Wen-Wei

    2012-01-01

    Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold. PMID:22415040

  18. Ant mound as an optimal shape in constructal design: solar irradiation and circadian brood/fungi-warming sorties.

    PubMed

    Kasimova, R G; Tishin, D; Obnosov, Yu V; Dlussky, G M; Baksht, F B; Kacimov, A R

    2014-08-21

    Sizes, shapes, ambient and in-dome temperature, incoming solar radiation and illumination are measured on a Formica rufa anthill in a mixed forest of the Volga-Kama National Reserve in Russia. These data are used in a conceptual model of insolation of a right conical surface by direct-beam, descending atmospheric and ascending ground-reflected radiation. Unlike a standard calculation of the energy flux intercepted by a solar panel, the anthill is a 3-D structure and double-integration of the cosine of the angle between the solar beams and normal to the surface is carried out for a "cozy trapezium", where the insects expose themselves and the brood to "morning" sunbathing pulses (Jones and Oldroyd, 2007). Several constructal design problems are formulated with the criteria involving either a pure solar energy gained by the dome or this energy, as a mathematical criterion, penalized by additive terms of mechanical energy (potential and friction) lost by the ants in their diurnal forays from a "heartland" of the nest to the sun-basking zone on the surface. The unique and global optima are analytically found, with the optimal tilt angle of the cone explicitly expressed through the zenith angle of the Sun and meteorological constants for the isotropic sky model.

  19. A Conceptual Framework for Procurement Decision Making Model to Optimize Supplier Selection: The Case of Malaysian Construction Industry

    NASA Astrophysics Data System (ADS)

    Chuan, Ngam Min; Thiruchelvam, Sivadass; Nasharuddin Mustapha, Kamal; Che Muda, Zakaria; Mat Husin, Norhayati; Yong, Lee Choon; Ghazali, Azrul; Ezanee Rusli, Mohd; Itam, Zarina Binti; Beddu, Salmia; Liyana Mohd Kamal, Nur

    2016-03-01

    This paper intends to fathom the current state of procurement system in Malaysia specifically in the construction industry in the aspect of supplier selection. This paper propose a comprehensive study on the supplier selection metrics for infrastructure building, weight the importance of each metrics assigned and to find the relationship between the metrics among initiators, decision makers, buyers and users. With the metrics hierarchy of criteria importance, a supplier selection process can be defined, repeated and audited with lesser complications or difficulties. This will help the field of procurement to improve as this research is able to develop and redefine policies and procedures that have been set in supplier selection. Developing this systematic process will enable optimization of supplier selection and thus increasing the value for every stakeholders as the process of selection is greatly simplified. With a new redefined policy and procedure, it does not only increase the company’s effectiveness and profit, but also make it available for the company to reach greater heights in the advancement of procurement in Malaysia.

  20. Optimal Use of Data in Parallel Tempering Simulations for the Construction of Discrete-State Markov Models of Biomolecular Dynamics

    SciTech Connect

    Prinz, Jan-Hendrik; Chondera, John D; Pande, Vijay S; Swope, William C; Smith, Jeremy C; Noe, F

    2011-01-01

    Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.

  1. Icosahedral medium-range orders and backbone formation in an amorphous alloy

    NASA Astrophysics Data System (ADS)

    Lee, Mirim; Kim, Hong-Kyu; Lee, Jae-Chul

    2010-12-01

    Analyses of metallic amorphous solids constructed using molecular dynamics (MD) simulations have demonstrated that individual short-range orders (SROs) are linked with neighboring SROs and form various medium-range orders (MROs). These MROs have been observed to have different structural stability depending on their linking patterns. On the basis of the assessment of the structural stability of various MROs, we propose new types of structural organization, namely, icosahedral medium-range orders (I-MROs) and their extended-range order that forms the backbone of amorphous solids. We also discuss why the atomic-scale structure of an amorphous alloy can be more appropriately described in terms of I-MROs, rather than by the degree of short-range ordering as characterized by the fractions of SROs.

  2. Photocaged G-Quadruplex DNAzyme and Aptamer by Post-Synthetic Modification on Phosphodiester Backbone.

    PubMed

    Feng, Mengli; Ruan, Zhiyuan; Shang, Jiachen; Xiao, Lu; Tong, Aijun; Xiang, Yu

    2017-02-15

    G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile post-synthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phosphodiester without any artificial scar. Similarly, the caged G-quadruplex thrombin-binding aptamer also showed light-induced activation of thrombin inhibition activity. This method could serve as a general strategy to prepare photocaged G-quadruplex DNA with other activities for noninvasive control of their functions.

  3. Using halogen bonds to address the protein backbone: a systematic evaluation.

    PubMed

    Wilcken, Rainer; Zimmermann, Markus O; Lange, Andreas; Zahn, Stefan; Boeckler, Frank M

    2012-08-01

    Halogen bonds are specific embodiments of the sigma hole bonding paradigm. They represent directional interactions between the halogens chlorine, bromine, or iodine and an electron donor as binding partner. Using quantum chemical calculations at the MP2 level, we systematically explore how they can be used in molecular design to address the omnipresent carbonyls of the protein backbone. We characterize energetics and directionality and elucidate their spatial variability in sub-optimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. By deriving simple rules, we aid medicinal chemists and chemical biologists in easily exploiting them for scaffold decoration and design. Our work shows that carbonyl-halogen bonds may be used to expand the patentable medicinal chemistry space, redefining halogens as key features. Furthermore, this data will be useful for implementing halogen bonds into pharmacophore models or scoring functions making the QM information available for automatic molecular recognition in virtual high throughput screening.

  4. "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

    PubMed

    Menéndez, C A; Accordino, S R; Gerbino, D C; Appignanesi, G A

    2015-10-01

    We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.

  5. Resistance of Feynman diagrams and the percolation backbone dimension.

    PubMed

    Janssen, H K; Stenull, O; Oerding, K

    1999-06-01

    We present an alternative view of Feynman diagrams for the field theory of random resistor networks, in which the diagrams are interpreted as being resistor networks themselves. This simplifies the field theory considerably as we demonstrate by calculating the fractal dimension D(B) of the percolation backbone to three loop order. Using renormalization group methods we obtain D(B)=2+epsilon/21-172epsilon(2)/9261+2epsilon(3)[-74 639+22 680zeta(3)]/4 084 101, where epsilon=6-d with d being the spatial dimension and zeta(3)=1.202 057... .

  6. A phylogenetic backbone for Bivalvia: an RNA-seq approach.

    PubMed

    González, Vanessa L; Andrade, Sónia C S; Bieler, Rüdiger; Collins, Timothy M; Dunn, Casey W; Mikkelsen, Paula M; Taylor, John D; Giribet, Gonzalo

    2015-02-22

    Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

  7. Long-term forecasting of internet backbone traffic.

    PubMed

    Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

    2005-09-01

    We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future.

  8. Construction of anthropomorphic hybrid, dual-lattice voxel models for optimizing image quality and dose in radiography

    NASA Astrophysics Data System (ADS)

    Petoussi-Henss, Nina; Becker, Janine; Greiter, Matthias; Schlattl, Helmut; Zankl, Maria; Hoeschen, Christoph

    2014-03-01

    In radiography there is generally a conflict between the best image quality and the lowest possible patient dose. A proven method of dosimetry is the simulation of radiation transport in virtual human models (i.e. phantoms). However, while the resolution of these voxel models is adequate for most dosimetric purposes, they cannot provide the required organ fine structures necessary for the assessment of the imaging quality. The aim of this work is to develop hybrid/dual-lattice voxel models (called also phantoms) as well as simulation methods by which patient dose and image quality for typical radiographic procedures can be determined. The results will provide a basis to investigate by means of simulations the relationships between patient dose and image quality for various imaging parameters and develop methods for their optimization. A hybrid model, based on NURBS (Non Linear Uniform Rational B-Spline) and PM (Polygon Mesh) surfaces, was constructed from an existing voxel model of a female patient. The organs of the hybrid model can be then scaled and deformed in a non-uniform way i.e. organ by organ; they can be, thus, adapted to patient characteristics without losing their anatomical realism. Furthermore, the left lobe of the lung was substituted by a high resolution lung voxel model, resulting in a dual-lattice geometry model. "Dual lattice" means in this context the combination of voxel models with different resolution. Monte Carlo simulations of radiographic imaging were performed with the code EGS4nrc, modified such as to perform dual lattice transport. Results are presented for a thorax examination.

  9. Evaluation of zinc-doped mesoporous hydroxyapatite microspheres for the construction of a novel biomimetic scaffold optimized for bone augmentation

    PubMed Central

    Yu, Weilin; Sun, Tuan-Wei; Qi, Chao; Ding, Zhenyu; Zhao, Huakun; Zhao, Shichang; Shi, Zhongmin; Zhu, Ying-Jie; Chen, Daoyun; He, Yaohua

    2017-01-01

    Biomaterials with high osteogenic activity are desirable for sufficient healing of bone defects resulting from trauma, tumor, infection, and congenital abnormalities. Synthetic materials mimicking the structure and composition of human trabecular bone are of considerable potential in bone augmentation. In the present study, a zinc (Zn)-doped mesoporous hydroxyapatite microspheres (Zn-MHMs)/collagen scaffold (Zn-MHMs/Coll) was developed through a lyophilization fabrication process and designed to mimic the trabecular bone. The Zn-MHMs were synthesized through a microwave-hydrothermal method by using creatine phosphate as an organic phosphorus source. Zn-MHMs that consist of hydroxyapatite nanosheets showed relatively uniform spherical morphology, mesoporous hollow structure, high specific surface area, and homogeneous Zn distribution. They were additionally investigated as a drug nanocarrier, which was efficient in drug delivery and presented a pH-responsive drug release behavior. Furthermore, they were incorporated into the collagen matrix to construct a biomimetic scaffold optimized for bone tissue regeneration. The Zn-MHMs/Coll scaffolds showed an interconnected pore structure in the range of 100–300 μm and a sustained release of Zn ions. More importantly, the Zn-MHMs/Coll scaffolds could enhance the osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells. Finally, the bone defect repair results of critical-sized femoral condyle defect rat model demonstrated that the Zn-MHMs/Coll scaffolds could enhance bone regeneration compared with the Coll or MHMs/Coll scaffolds. The results suggest that the biomimetic Zn-MHMs/Coll scaffolds may be of enormous potential in bone repair and regeneration. PMID:28392688

  10. Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation

    PubMed Central

    Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D.; Xia, Lan-Qin

    2016-01-01

    Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation will be useful to facilitate the creation of “clean” GM wheat containing only the foreign genes of agronomic importance. PMID:27708648

  11. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

    PubMed

    Gront, Dominik; Kmiecik, Sebastian; Kolinski, Andrzej

    2007-07-15

    In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.

  12. Optimal flux patterns in cellular metabolic networks

    SciTech Connect

    Almaas, E

    2007-01-20

    The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central-carbon metabolic pathways for the sample of random environments.

  13. Optimal flux patterns in cellular metabolic networks

    NASA Astrophysics Data System (ADS)

    Almaas, Eivind

    2007-06-01

    The availability of whole-cell-level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate the metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30 000 random cellular environments. The distribution of reaction fluxes is heavy tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations has relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reactions are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central carbon metabolic pathways for the sample of random environments.

  14. Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

    PubMed

    Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

    2015-06-05

    Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function.

  15. Reconstruction of the Sunspot Group Number: The Backbone Method

    NASA Astrophysics Data System (ADS)

    Svalgaard, Leif; Schatten, Kenneth H.

    2016-11-01

    We have reconstructed the sunspot-group count, not by comparisons with other reconstructions and correcting those where they were deemed to be deficient, but by a re-assessment of original sources. The resulting series is a pure solar index and does not rely on input from other proxies, e.g. radionuclides, auroral sightings, or geomagnetic records. "Backboning" the data sets, our chosen method, provides substance and rigidity by using long-time observers as a stiffness character. Solar activity, as defined by the Group Number, appears to reach and sustain for extended intervals of time the same level in each of the last three centuries since 1700 and the past several decades do not seem to have been exceptionally active, contrary to what is often claimed.

  16. Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.

    PubMed

    Azoitei, Mihai L; Ban, Yih-En Andrew; Julien, Jean-Philippe; Bryson, Steve; Schroeter, Alexandria; Kalyuzhniy, Oleksandr; Porter, Justin R; Adachi, Yumiko; Baker, David; Pai, Emil F; Schief, William R

    2012-01-06

    Computational grafting of functional motifs onto scaffold proteins is a promising way to engineer novel proteins with pre-specified functionalities. Typically, protein grafting involves the transplantation of protein side chains from a functional motif onto structurally homologous regions of scaffold proteins. Using this approach, we previously transplanted the human immunodeficiency virus 2F5 and 4E10 epitopes onto heterologous proteins to design novel "epitope-scaffold" antigens. However, side-chain grafting is limited by the availability of scaffolds with compatible backbone for a given epitope structure and offers no route to modify backbone structure to improve mimicry or binding affinity. To address this, we report here a new and more aggressive computational method-backbone grafting of linear motifs-that transplants the backbone and side chains of linear functional motifs onto scaffold proteins. To test this method, we first used side-chain grafting to design new 2F5 epitope scaffolds with improved biophysical characteristics. We then independently transplanted the 2F5 epitope onto three of the same parent scaffolds using the newly developed backbone grafting procedure. Crystal structures of side-chain and backbone grafting designs showed close agreement with both the computational models and the desired epitope structure. In two cases, backbone grafting scaffolds bound antibody 2F5 with 30- and 9-fold higher affinity than corresponding side-chain grafting designs. These results demonstrate that flexible backbone methods for epitope grafting can significantly improve binding affinities over those achieved by fixed backbone methods alone. Backbone grafting of linear motifs is a general method to transplant functional motifs when backbone remodeling of the target scaffold is necessary.

  17. Pendant Dynamics of Ethylene-Oxide Containing Polymers with Diverse Backbones

    NASA Astrophysics Data System (ADS)

    Bartels, Joshua; Wang, Jing-Han Helen; Chen, Quan; Runt, James; Colby, Ralph

    In the last twenty years, a wide variety of ion conducting polymers have used ether oxygens to facilitate ion conduction, and it is therefore important to understand the dynamics of ether oxygens (EOs) when attached to different polymer backbones. Four different EO-containing polymer architectures are studied by dielectric spectroscopy to understand the backbone effect on the EO dipoles. Polysiloxanes, polyphosphazenes, polymethylmethacrylates, and a polyester ether are compared, with different EO pendant lengths for the siloxane and methylmethacrylate backbones. The flexible polysiloxanes and polyphosphazene backbones impart superior segmental mobility with a glass transition temperature 15 K lower than that of the organic backbone polymers. Short EO pendants are found to impart a lower static dielectric constant at comparable EO content as compared to longer EO pendants of either inorganic or organic backbones. The long-pendant polymethylmethacrylate polymers show two relaxations corresponding to fast EOs near the pendant tail end and slow EOs close to the slower backbone, whereas the long-pendant polysiloxane shows a single relaxation due to the siloxane backbone relaxing faster than the EO pendant. Supported by the NSF Division of Materials Research Polymers Program through Grants DMR-1404586 (RHC) and DMR-1505953 (JR).

  18. Backbone of complex networks of corporations: The flow of control

    NASA Astrophysics Data System (ADS)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  19. Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

    PubMed

    Unnerståle, Sofia; Nowakowski, Michal; Baraznenok, Vera; Stenberg, Gun; Lindberg, Jimmy; Mayzel, Maxim; Orekhov, Vladislav; Agback, Tatiana

    2016-01-01

    Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15)N/(13)C/(1)H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.

  20. Thermogelling Biodegradable Polymers with Hydrophilic Backbones: PEG-g-PLGA

    SciTech Connect

    Jeong, Byeongmoon; Kibbey, Merinda R.; Birnbaum, Jerome C.; Won, You-Yeong; Gutowska, Anna

    2000-10-31

    The aqueous solutions of poly(ethylene glycol)grafted with poly(lactic acid-co-glycolic acid) flow freely at room temperature but form gels at higher temperature. The existence of micelles in water at low polymer concentration was confirmed by Cro-transmission electron microscopy and dye solubilization studies. The micellar diameter and critical micelle concentration are about 9 nm and 0.47 wt.% respectively. The critical gel concentration, above which a gel phase appears was 16 wt.% and sol-to-gel transition temperature was slightly affected by the concentration in the range of 16 {approx} 25 wt.%. At sol-to-gel transition, viscosity increased abruptly and C-NMR showed molecular motion of hydrophilic poly(lactic acid-co-glycolic acid) side-chains increased. The hydrogel of PEG-g-PLGA with hydrophilic backbones was transparent during degradation and remained a gel for one week, suggesting a promising material for short-term drug delivery.

  1. Backbone Assignment of the MALT1 Paracaspase by Solution NMR

    PubMed Central

    Unnerståle, Sofia; Nowakowski, Michal; Baraznenok, Vera; Stenberg, Gun; Lindberg, Jimmy; Mayzel, Maxim; Orekhov, Vladislav; Agback, Tatiana

    2016-01-01

    Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the 15N/13C/1H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins. PMID:26788853

  2. Backbone of complex networks of corporations: the flow of control.

    PubMed

    Glattfelder, J B; Battiston, S

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  3. Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs

    PubMed Central

    Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P.; Schrooten, Jan; Geris, Liesbet

    2015-01-01

    To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial ‘design of experiments’ approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology. PMID:26076131

  4. Optimism Reborn. Nicaragua's Participative Education Revolution, the Citizen Power Development Model and the Construction of "21st Century Socialism"

    ERIC Educational Resources Information Center

    Muhr, Thomas

    2013-01-01

    This paper explores Nicaragua's Participative Education Revolution and the Citizen Power national development model in the construction of socialism in the 21st century in Latin America and the Caribbean through the Bolivarian Alliance for the Peoples of Our America--Peoples' Trade Agreement. Centred around the notion of "revolutionary…

  5. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue

    PubMed Central

    Revilla-López, Guillem; Torras, Juan; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos

    2009-01-01

    The intrinsic conformational preferences of the non-proteinogenic amino acids constructed by incorporating the arginine side chain in the β position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c5Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N′-methylamide derivatives of cis and trans-c5Arg have been examined in the gas phase and in solution using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen-bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented. PMID:19236034

  6. Proteins of well-defined structures can be designed without backbone readjustment by a statistical model.

    PubMed

    Zhou, Xiaoqun; Xiong, Peng; Wang, Meng; Ma, Rongsheng; Zhang, Jiahai; Chen, Quan; Liu, Haiyan

    2016-12-01

    We report that using mainly a statistical energy model, protein sequence design for designable backbones can be carried out with high confidence without considering backbone relaxation. A recently-developed statistical energy function for backbone-based protein sequence design has been rationally revised to improve its accuracy. As a demonstrative example, this revised model is applied to design a de novo protein for a target backbone for which the previous model had relied on after-design directed evolution to produce a well-folded protein. The actual backbone structure of the newly designed protein agrees excellently with the corresponding target. Besides presenting a new protein design protocol with experimentally verifications on different backbone types, our study implies that with an energy model of an appropriate resolution, proteins of well-defined structures instead of molten globules can be designed without the explicit consideration of backbone variations due to side chain changes, even if the side chain changes correspond to complete sequence redesigns.

  7. Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

    NASA Astrophysics Data System (ADS)

    Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

    2011-10-01

    Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

  8. Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

    SciTech Connect

    Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R.

    2012-02-07

    The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

  9. Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

    PubMed

    Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

    2014-10-30

    Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org.

  10. [Generation of vector backbone-free and selectable marker-free transgenic maize (Zea mays L.) via ovary-drip method].

    PubMed

    Yang, Ai-Fu; Su, Qiao; An, Li-Jia

    2009-01-01

    The presence of vector backbone sequences and selectable marker genes in transgenic plants has been the key concern for biosafety. A direct solution is to totally avoid the use of vector backbone sequences and selectable marker genes from the beginning of transgenic plant generation. In this study, the ovary-drip method was established and optimized. The key features of this method focused on the complete removal of the whole styles, and the subsequent application of a DNA solution directly to the ovaries. A vector backbone-free and selectable marker-free linear GFP cassette (Ubi-GFP -nos) was transformed into maize via the ovary-drip method. PCR analysis showed that suitable maize variety was 9818 and optimal transformation time was 18-20 h after pollination, which produced the highest PCR positive frequency (3.01%). Southern blotting analysis showed that the transgenic plants had simple integration patterns (1-2 bands). GFP transcription was de-tected by RT-PCR analysis. Green fluorescence was observed in roots and immature embryos of transgenic plants by a fluorescence microscopy.

  11. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid

    PubMed Central

    Babbitt, Gregory A.; Alawad, Mohammed A.; Schulze, Katharina V.; Hudson, André O.

    2014-01-01

    While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. PMID:25200075

  12. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

    PubMed

    Babbitt, Gregory A; Alawad, Mohammed A; Schulze, Katharina V; Hudson, André O

    2014-01-01

    While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.

  13. Multi-source micro-friction identification for a class of cable-driven robots with passive backbone

    NASA Astrophysics Data System (ADS)

    Tjahjowidodo, Tegoeh; Zhu, Ke; Dailey, Wayne; Burdet, Etienne; Campolo, Domenico

    2016-12-01

    This paper analyses the dynamics of cable-driven robots with a passive backbone and develops techniques for their dynamic identification, which are tested on the H-Man, a planar cabled differential transmission robot for haptic interaction. The mechanism is optimized for human-robot interaction by accounting for the cost-benefit-ratio of the system, specifically by eliminating the necessity of an external force sensor to reduce the overall cost. As a consequence, this requires an effective dynamic model for accurate force feedback applications which include friction behavior in the system. We first consider the significance of friction in both the actuator and backbone spaces. Subsequently, we study the required complexity of the stiction model for the application. Different models representing different levels of complexity are investigated, ranging from the conventional approach of Coulomb to an advanced model which includes hysteresis. The results demonstrate each model's ability to capture the dynamic behavior of the system. In general, it is concluded that there is a trade-off between model accuracy and the model cost.

  14. Construct optimization for studying protein complexes: obtaining diffraction-quality crystals of the pseudosymmetric PSPC1-NONO heterodimer.

    PubMed

    Lee, Mihwa; Passon, Daniel M; Hennig, Sven; Fox, Archa H; Bond, Charles S

    2011-11-01

    The methodology of protein crystallography provides a number of potential bottlenecks. Here, an approach to successful structure solution of a difficult heterodimeric complex of two human proteins, paraspeckle component 1 (PSPC1) and non-POU domain-containing octamer-binding protein (NONO), that are involved in gene regulation and the structural integrity of nuclear bodies termed paraspeckles is described. With the aid of bioinformatic predictions and systematic screening of a panel of constructs, bottlenecks of protein solubility, crystallization, crystal quality and crystallographic pseudosymmetry were overcome in order to produce crystals that ultimately revealed the structure.

  15. [Obtaining marker-free transgenic soybean plants with optimal frequency by constructing three T-DNAs binary vector].

    PubMed

    Ye, Xing-Guo; Qin, Hua

    2007-01-01

    Obtaining marker-free plants with high efficiency will benefit the environmental release of transgenic crops. To achieve this point, a binary vector pNB35SVIP1 with three T-DNAs was constructed by using several mediate plasmids, in which one copy of bar gene expression cassette and two copies of VIP1 gene expression cassette were included. EHA101 Agrobacterium strain harboring the final construct was applied to transform soybean (Glycine max) cotyledon nodes. Through 2 - 3 months regeneration and selection on 3 - 5mg/L glufosinate containing medium, transgenic soybean plants were confirmed to be obtained at 0.83% - 3.16%, and co-transformation efficiency of both gene in the same individual reached up to 86.4%, based on southern blot test. By the analysis of PCR, southern blot and northern blot combining with leaf painting of herbicide in T1 progenies, 41 plants were confirmed to be eliminated of bar gene with the frequency of 7.6% . Among the T1 populations tested, the loss of the alien genes happened in 22.7% lines, the silence of bar gene took place in 27.3% lines, and VIP1 gene silence existed in 37.1% marker-free plants. The result also suggested that the plasmid with three T-DNAs might be an ideal vector to generate maker-free genetic modified organism.

  16. Modeling 15N NMR chemical shift changes in protein backbone with pressure

    NASA Astrophysics Data System (ADS)

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-01

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  17. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    SciTech Connect

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  18. Modeling (15)N NMR chemical shift changes in protein backbone with pressure.

    PubMed

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-28

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  19. A simple model of backbone flexibility improves modeling of side-chain conformational variability.

    PubMed

    Friedland, Gregory D; Linares, Anthony J; Smith, Colin A; Kortemme, Tanja

    2008-07-18

    The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may have a role in mediating allosteric interactions. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods frequently keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here, we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from nuclear magnetic resonance (NMR) experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high-resolution X-ray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant improvements in modeling side-chain order parameters for ten of the 17 proteins in the set. Greater accuracy of the flexible backbone model results from both increases and decreases in side-chain flexibility relative to the fixed-backbone model. This simple flexible-backbone model should be useful for a variety of protein design applications, including improved modeling of protein-protein interactions, design of proteins with desired flexibility or rigidity, and prediction of correlated motions within proteins.

  20. Optimal sequence selection in proteins of known structure by simulated evolution.

    PubMed Central

    Hellinga, H W; Richards, F M

    1994-01-01

    Rational design of protein structure requires the identification of optimal sequences to carry out a particular function within a given backbone structure. A general solution to this problem requires that a potential function describing the energy of the system as a function of its atomic coordinates be minimized simultaneously over all available sequences and their three-dimensional atomic configurations. Here we present a method that explicitly minimizes a semiempirical potential function simultaneously in these two spaces, using a simulated annealing approach. The method takes the fixed three-dimensional coordinates of a protein backbone and stochastically generates possible sequences through the introduction of random mutations. The corresponding three-dimensional coordinates are constructed for each sequence by "redecorating" the backbone coordinates of the original structure with the corresponding side chains. These are then allowed to vary in their structure by random rotations around free torsional angles to generate a stochastic walk in configurational space. We have named this method protein simulated evolution, because, in loose analogy with natural selection, it randomly selects for allowed solutions in the sequence of a protein subject to the "selective pressure" of a potential function. Energies predicted by this method for sequences of a small group of residues in the hydrophobic core of the phage lambda cI repressor correlate well with experimentally determined biological activities. This "genetic selection by computer" approach has potential applications in protein engineering, rational protein design, and structure-based drug discovery. PMID:8016069

  1. Optimal construction of a fast and accurate polarisable water potential based on multipole moments trained by machine learning.

    PubMed

    Handley, Chris M; Hawe, Glenn I; Kell, Douglas B; Popelier, Paul L A

    2009-08-14

    To model liquid water correctly and to reproduce its structural, dynamic and thermodynamic properties warrants models that account accurately for electronic polarisation. We have previously demonstrated that polarisation can be represented by fluctuating multipole moments (derived by quantum chemical topology) predicted by multilayer perceptrons (MLPs) in response to the local structure of the cluster. Here we further develop this methodology of modeling polarisation enabling control of the balance between accuracy, in terms of errors in Coulomb energy and computing time. First, the predictive ability and speed of two additional machine learning methods, radial basis function neural networks (RBFNN) and Kriging, are assessed with respect to our previous MLP based polarisable water models, for water dimer, trimer, tetramer, pentamer and hexamer clusters. Compared to MLPs, we find that RBFNNs achieve a 14-26% decrease in median Coulomb energy error, with a factor 2.5-3 slowdown in speed, whilst Kriging achieves a 40-67% decrease in median energy error with a 6.5-8.5 factor slowdown in speed. Then, these compromises between accuracy and speed are improved upon through a simple multi-objective optimisation to identify Pareto-optimal combinations. Compared to the Kriging results, combinations are found that are no less accurate (at the 90th energy error percentile), yet are 58% faster for the dimer, and 26% faster for the pentamer.

  2. Optimization of the bamboo guadua angustifolia kunth in the elaboration of glued laminated elements for constructive use

    NASA Astrophysics Data System (ADS)

    Díaz, G. A.; Cruz, R. A.; Chávez, A. M.

    2013-11-01

    Bamboo is considered one of the best timber resources in the world because for its mechanical properties and high sustainability; this research aims to improve the mechanical properties of the laminated glued bamboo Guadua Angustifolia Kunth (GAK) for use as structural elements, starting from de very manufacture process; this is important because it is possible to observe variations in the flexural strength and the elastic modulus in GAK samples taken from different heights and thickness of the culm. In order to analyze the influence of these final mechanical properties variations in the laminated, the height of the culm where samples are extracted (cepa, basa and sobrebasa) it is taken as a variable from where different types of laminated were manufactured, seeking to make optimal the configuration based in the transversal section area and the material strength. Three assemblies were designed varying the overlap of the adhesion lines and it concluded that the highest strength average values were obtained in the laminated composites manufactured with samples taken from the bottom of the culm (basa), which is possible because in these elements there are less adhesion lines than the other ones (middle, top and mixed) or the better matching of themselves.

  3. Construction of high-resolution stochastic geological models and optimal upscaling to a simplified layer-type hydrogeological model

    NASA Astrophysics Data System (ADS)

    Quental, Paulo; Almeida, José António; Simões, Manuela

    2012-04-01

    Despite inequalities in spatial resolution between stochastic geological models and flow simulator models, geostatistical algorithms are used for the characterisation of groundwater systems. From available data to grid-block hydraulic parameters, workflows basically utilise the development of a detailed geostatistical model (morphology and properties) followed by upscaling. This work aims to design and test a two-step methodology encompassing the generation of a high-resolution 3D stochastic geological model and simplification into a low-resolution groundwater layer-type model. First, a high-resolution 3D stochastic model of rock types or hydrofacies (sets of rock types with similar hydraulic characteristics) is generated using an enhanced version of the sequential indicator simulation (SIS) with corrections for local probabilities and for two- and three-point template statistics. In a second step, the high-resolution geological model provided by SIS is optimally simplified into a small set of layers according to a supervised simulated annealing (SA) optimisation procedure and at the end equivalent hydraulic properties are upscaled. Two outcomes are provided by this methodology: (1) a regular 2D mesh of the top and bottom limits of each hydrogeological unit or layer from a conceptual model and (2), for each layer, a 2D grid-block of equivalent hydraulic parameters prepared to be inputted into an aquifer simulator. This methodology was tested for the upper aquifer area of SPEL (Sociedade Portuguesa de Explosivos), an explosives deactivation plant in Seixal municipality, Portugal.

  4. Combining dehydration, construct optimization and improved data collection to solve the crystal structure of a CRM1-RanGTP-SPN1-Nup214 quaternary nuclear export complex.

    PubMed

    Monecke, Thomas; Dickmanns, Achim; Weiss, Manfred S; Port, Sarah A; Kehlenbach, Ralph H; Ficner, Ralf

    2015-12-01

    High conformational flexibility is an intrinsic and indispensable property of nuclear transport receptors, which makes crystallization and structure determination of macromolecular complexes containing exportins or importins particularly challenging. Here, the crystallization and structure determination of a quaternary nuclear export complex consisting of the exportin CRM1, the small GTPase Ran in its GTP-bound form, the export cargo SPN1 and an FG repeat-containing fragment of the nuclear pore complex component nucleoporin Nup214 fused to maltose-binding protein is reported. Optimization of constructs, seeding and the development of a sophisticated protocol including successive PEG-mediated crystal dehydration as well as additional post-mounting steps were essential to obtain well diffracting crystals.

  5. Evaluating the performance of CMIP5 GCMs in Northern Eurasia and constructing optimal ensemble projection: analysis of regional precipitation patterns (Invited)

    NASA Astrophysics Data System (ADS)

    Kokorev, V.; Anisimov, O. A.

    2013-12-01

    Despite significant improvements in the complexity and quality of the global climate models, even the most recent CMIP-5 GCMs differ in results at regional scale. Several studies have tried to assess and quantify the uncertainties of temperature and atmospheric pressure parameters, while the evaluation of precipitation parameters at regional scale is yet to be done. The goal of this study is to perform comprehensive analysis of precipitation uncertainty for Northern Eurasia. To accomplish this goal we contrast selected precipitation parameters from two generations of CMIP5 and CMIP3 GCMs with observations at regional level and suggest the methodology for constructing the optimal ensemble projection. We used data from 744 Russian weather stations to identify 14 regions in Northern Eurasia characterized by coherent changes of temperature characteristics and precipitation. In each region we identified the tipping point, which divide timeseries into baseline period and period of contemporary climate change, and tested the ability of GCMs to simulate precipitation patterns and trends in each region. Ultimately, we ranked GCMs according to their performance in representing regional precipitation parameters. We used this ranking to construct several regional ensembles consisting of different number of high-ranked models and compared results from these optimized ensembles with observations and with the ensemble of all models. The ultimate conclusion of our study is that the methodology based on pre-selection of top ranked models allows narrowing the range of uncertainty in climate projection at regional level. With latest generation of GCMs this methodology could be applied not only to air temperature but also to precipitation parameters. We also found that models from CMIP5 generation demonstrate much higher performance than CMIP3 models in replicating precipitation parameters in the period of contemporary climate change. Acknowledgement. This study is supported by the

  6. Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Olea europaea L.) Genetic Resources

    PubMed Central

    El Bakkali, Ahmed; Haouane, Hicham; Moukhli, Abdelmajid; Costes, Evelyne; Van Damme, Patrick; Khadari, Bouchaib

    2013-01-01

    Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species. PMID:23667437

  7. Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea L.) genetic resources.

    PubMed

    El Bakkali, Ahmed; Haouane, Hicham; Moukhli, Abdelmajid; Costes, Evelyne; Van Damme, Patrick; Khadari, Bouchaib

    2013-01-01

    Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species.

  8. The multiscale backbone of the human phenotype network based on biological pathways

    PubMed Central

    2014-01-01

    Background Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic background. We built pathway-based human phenotype network (PHPN) of over 800 physical attributes, diseases, and behavioral traits; based on about 2,300 genes and 1,200 biological pathways. Using GWAS phenotype-to-genes associations, and pathway data from Reactome, we connect human traits based on the common patterns of human biological pathways, detecting more pleiotropic effects, and expanding previous studies from a gene-centric approach to that of shared cell-processes. Results The resulting network has a heavily right-skewed degree distribution, placing it in the scale-free region of the network topologies spectrum. We extract the multi-scale information backbone of the PHPN based on the local densities of the network and discarding weak connection. Using a standard community detection algorithm, we construct phenotype modules of similar traits without applying expert biological knowledge. These modules can be assimilated to the disease classes. However, we are able to classify phenotypes according to shared biology, and not arbitrary disease classes. We present examples of expected clinical connections identified by PHPN as proof of principle. Conclusions We unveil a previously uncharacterized connection between phenotype modules and discuss potential mechanistic connections that are obvious only in retrospect. The PHPN shows tremendous potential to become a useful tool both in the unveiling of the diseases’ common biology, and in the elaboration of diagnosis and treatments. PMID:24460644

  9. Bio-cathode materials evaluation and configuration optimization for power output of vertical subsurface flow constructed wetland - microbial fuel cell systems.

    PubMed

    Liu, Shentan; Song, Hailiang; Wei, Size; Yang, Fei; Li, Xianning

    2014-08-01

    To optimize the performance of a vertical subsurface flow constructed wetland-microbial fuel cell (CW-MFC), studies of bio-cathode materials and reactor configurations were carried out. Three commonly used bio-cathode materials including stainless steel mesh (SSM), carbon cloth (CC) and granular activated carbon (GAC) were compared and evaluated. GAC-SSM bio-cathode achieved the highest maximum power density of 55.05 mWm(-2), and it was most suitable for CW-MFCs application because of its large surface area and helpful capillary water absorption. Two types of CW-MFCs with roots were constructed, one was placed in the anode and the other was placed in the cathode. Both planted CW-MFCs obtained higher power output than non-planted CW-MFC. Periodic voltage fluctuations of planted CW-MFCs were caused by light/dark cycles, and the influent substrate concentration significantly affected the amplitude of oscillation. The coulombic efficiencies of CW-MFCs decreased greatly with the increase of the influent substrate concentration.

  10. Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11.

    PubMed

    Fowler, Melissa L; McPhail, Jacob A; Jenkins, Meredith L; Masson, Glenn R; Rutaganira, Florentine U; Shokat, Kevan M; Williams, Roger L; Burke, John E

    2016-04-01

    The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIβ) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches.

  11. Quantitative 2D and 3D Gamma-HCP experiments for the determination of the angles alpha and zeta in the phosphodiester backbone of oligonucleotides.

    PubMed

    Nozinovic, Senada; Richter, Christian; Rinnenthal, Jörg; Fürtig, Boris; Duchardt-Ferner, Elke; Weigand, Julia E; Schwalbe, Harald

    2010-08-04

    The quantitative Gamma-(HCP) experiment, a novel heteronuclear NMR pulse sequence for the determination of the RNA backbone angles alpha(O3'(i-1)-P(i)-O5'(i)-C5'(i)) and zeta(C3'(i)-O3'(i)-P(i+1)-O5'(i+1)) in (13)C-labeled RNA, is introduced. The experiment relies on the interaction between the CH bond vector dipole and the (31)P chemical shift anisotropy (CSA), which affects the relaxation of the (13)C,(31)P double- and zero-quantum coherence and thus the intensity of the detectable magnetization. With the new pulse sequence, five different cross-correlated relaxation rates along the phosphodiester backbone can be measured in a quantitative manner, allowing projection-angle and torsion-angle restraints for the two backbone angles alpha and zeta to be extracted. Two versions of the pulse sequence optimized for the CH and CH(2) groups are introduced and demonstrated for a 14-mer cUUCGg tetraloop RNA model system and for a 27-mer RNA with a previously unknown structure. The restraints were incorporated into the calculation of a very high resolution structure of the RNA model system (Nozinovic, S.; et al. Nucleic Acids Res. 2010, 38, 683). Comparison with the X-ray structure of the cUUCGg tetraloop confirmed the high quality of the data, suggesting that the method can significantly improve the quality of RNA structure determination.

  12. Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses.

    PubMed

    Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nantawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

    2012-02-14

    Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby canine kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 2(9) HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems.

  13. Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect.

    PubMed Central

    Gunner, M R; Saleh, M A; Cross, E; ud-Doula, A; Wise, M

    2000-01-01

    Asymmetry in packing the peptide amide dipole results in larger positive than negative regions in proteins of all folding motifs. The average side chain potential in 305 proteins is 109 +/- 30 mV (2. 5 +/- 0.7 kcal/mol/e). Because the backbone has zero net charge, the non-zero potential is unexpected. The larger oxygen at the negative and smaller proton at the positive end of the amide dipole yield positive potentials because: 1) at allowed phi and psi angles residues come off the backbone into the positive end of their own amide dipole, avoiding the large oxygen; and 2) amide dipoles with their carbonyl oxygen surface exposed and amine proton buried make the protein interior more positive. Twice as many amides have their oxygens exposed than their amine protons. The distribution of acidic and basic residues shows the importance of the bias toward positive backbone potentials. Thirty percent of the Asp, Glu, Lys, and Arg are buried. Sixty percent of buried residues are acids, only 40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by >3 pH units (-4.1 kcal/mol). Only 6.5% of the bases are equivalently stabilized by negative regions. The backbone stabilizes bound anions such as phosphates and rarely stabilizes bound cations. PMID:10692303

  14. Subgraph "backbone" analysis of dynamic brain networks during consciousness and anesthesia.

    PubMed

    Shin, Jeongkyu; Mashour, George A; Ku, Seungwoo; Kim, Seunghwan; Lee, Uncheol

    2013-01-01

    General anesthesia significantly alters brain network connectivity. Graph-theoretical analysis has been used extensively to study static brain networks but may be limited in the study of rapidly changing brain connectivity during induction of or recovery from general anesthesia. Here we introduce a novel method to study the temporal evolution of network modules in the brain. We recorded multichannel electroencephalograms (EEG) from 18 surgical patients who underwent general anesthesia with either propofol (n = 9) or sevoflurane (n = 9). Time series data were used to reconstruct networks; each electroencephalographic channel was defined as a node and correlated activity between the channels was defined as a link. We analyzed the frequency of subgraphs in the network with a defined number of links; subgraphs with a high probability of occurrence were deemed network "backbones." We analyzed the behavior of network backbones across consciousness, anesthetic induction, anesthetic maintenance, and two points of recovery. Constitutive, variable and state-specific backbones were identified across anesthetic state transitions. Brain networks derived from neurophysiologic data can be deconstructed into network backbones that change rapidly across states of consciousness. This technique enabled a granular description of network evolution over time. The concept of network backbones may facilitate graph-theoretical analysis of dynamically changing networks.

  15. Fast extraction of the backbone of projected bipartite networks to aid community detection

    NASA Astrophysics Data System (ADS)

    Liebig, J.; Rao, A.

    2016-01-01

    This paper introduces a computationally inexpensive method for extracting the backbone of one-mode networks projected from bipartite networks. We show that the edge weights in the one-mode projections are distributed according to a Poisson binomial distribution and that finding the expected weight distribution of a one-mode network projected from a random bipartite network only requires knowledge of the bipartite degree distributions. Being able to extract the backbone of a projection is highly beneficial in filtering out redundant information in large complex networks and narrowing down the information in the one-mode projection to the most relevant. We demonstrate that the backbone of a one-mode projection aids in the detection of communities.

  16. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    PubMed

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation.

  17. No-Enclave Percolation Corresponds to Holes in the Cluster Backbone

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Ziff, Robert M.; Deng, Youjin

    2016-10-01

    The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ =1.82 (1 ) as found for the NEP model. An argument is given that τ =1 +dB/2 ≈1.822 for backbone holes, where dB is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ =1 +df/2 =187 /96 ≈1.948 , where df is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ =1.91 (6 ). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at pc, signifying explosive percolation behavior.

  18. Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.

    PubMed

    Chen, Meng-Yun; Liang, Dan; Zhang, Peng

    2015-11-01

    Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes.

  19. Ebolavirus VP35 Coats the Backbone of Double-Stranded RNA for Interferon Antagonism

    PubMed Central

    Bale, Shridhar; Julien, Jean-Philippe; Bornholdt, Zachary A.; Krois, Alexander S.; Wilson, Ian A.

    2013-01-01

    Recognition of viral double-stranded RNA (dsRNA) activates interferon production and immune signaling in host cells. Crystal structures of ebolavirus VP35 show that it caps dsRNA ends to prevent sensing by pattern recognition receptors such as RIG-I. In contrast, structures of marburgvirus VP35 show that it primarily coats the dsRNA backbone. Here, we demonstrate that ebolavirus VP35 also coats the dsRNA backbone in solution, although binding to the dsRNA ends probably constitutes the initial binding event. PMID:23824825

  20. Solvation thermodynamics of amino acid side chains on a short peptide backbone

    SciTech Connect

    Hajari, Timir; Vegt, Nico F. A. van der

    2015-04-14

    The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side

  1. Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

    PubMed Central

    Feagin, Trevor A.; Shah, Nirmal I.; Heemstra, Jennifer M.

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. PMID:22848796

  2. Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

    NASA Astrophysics Data System (ADS)

    Shew, Christopher; Evans, Samari; Tao, Xiuping

    How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

  3. Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

    NASA Astrophysics Data System (ADS)

    Maesano, Francesco E.; D'Ambrogi, Chiara

    2017-02-01

    We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

  4. The Zurich Tradition: Backbone of the Wolf Number Series (Invited)

    NASA Astrophysics Data System (ADS)

    Friedli, T. K.

    2013-12-01

    The Wolf Series of Sunspot Relative Numbers is divided into a more recent part starting from 1849 up to present which is based on dedicated visual observations and into a reconstructed part reaching back to the mythological ages of Galileo, Harriot and Scheiner which is based solely on indirect countings made from drawings or texts from various archives. The Zurich tradition consists of a framework of rules and prerequisites concerning the quality and power of the instrumentation, the observation and counting techniques, the methods for calibration and preservation of scale and the construction of a long-term record. This framework guarantees the homogeneity of the series and the preservation of the original scale. In the modern part of the series up to 1980, the published Wolf numbers are based in over 90% of the days on calibrated visual observations of the original Fraunhofer refractor. The long term preservation of the original scale is thus mainly determined by the quality and validity of the calibration from one generation of standard observers to the next and on the internal consistency of the individual observing and counting methods of each standard observer. Since 1996 the historical standard refractor of Rudolf Wolf, in succession of the Zurich observers, has been used by the author for the daily determination of the sunspot relative number. With the aid of a small network of keen amateur astronomers of the Rudolf Wolf Gesellschaft these observations could be calibrated to the former Zurich scale. This results in an extension of the original Zurich series which is independent from the official one by SIDC or from the one by AAVSO. The main lesson learned from this exercise is that calibration functions reduce to simple proportionality factors as long as the calculations are made within a proper statistical regression framework over a sufficiently long evaluation period covering both maximum and minimum activity phases. Based on the original observations

  5. Improved Generation of Induced Cardiomyocytes Using a Polycistronic Construct Expressing Optimal Ratio of Gata4, Mef2c and Tbx5

    PubMed Central

    Wang, Li; Liu, Ziqing; Yin, Chaoying; Zhou, Yang; Liu, Jiandong; Qian, Li

    2017-01-01

    Direct conversion of cardiac fibroblasts (CFs) into induced cardiomyocytes (iCMs) holds great potential for regenerative medicine by offering alternative strategies for treatment of heart disease. This conversion has been achieved by forced expression of defined factors such as Gata4 (G), Mef2c (M) and Tbx5 (T). Traditionally, iCMs are generated by a cocktail of viruses expressing these individual factors. However, reprogramming efficiency is relatively low and most of the in vitro G,M,T-transduced fibroblasts do not become fully reprogrammed, making it difficult to study the reprogramming mechanisms. We recently have shown that the stoichiometry of G,M,T is crucial for efficient iCM reprogramming. An optimal stoichiometry of G,M,T with relative high level of M and low levels of G and T achieved by using our polycistronic MGT vector (hereafter referred to as MGT) significantly increased reprogramming efficiency and improved iCM quality in vitro. Here we provide a detailed description of the methodology used to generate iCMs with MGT construct from cardiac fibroblasts. Isolation of cardiac fibroblasts, generation of virus for reprogramming and evaluation of the reprogramming process are also included to provide a platform for efficient and reproducible generation of iCMs. PMID:26649751

  6. Effects of Protein Stabilizing Agents on Thermal Backbone Motions: A Disulfide Trapping Study†

    PubMed Central

    Butler, Scott L.; Falke, Joseph J.

    2010-01-01

    Chemical stabilizers are widely used to enhance protein stability, both in nature and in the laboratory. Here, the molecular mechanism of chemical stabilizers is studied using a disulfide trapping assay to measure the effects of stabilizers on thermal backbone dynamics in the Escherichia coli galactose/glucose binding protein. Two types of backbone fluctuations are examined: (a) relative movements of adjacent surface α-helices within the same domain and (b) interdomain twisting motions. Both types of fluctuations are significantly reduced by all six stabilizers tested (glycerol, sucrose, trehalose, l-glucose, d-glucose, and d-galactose), and in each case larger amplitude motions are inhibited more than smaller ones. Motional inhibition does not require a high-affinity stabilizer binding site, indicating that the effects of stabilizers are nonspecific. Overall, the results support the theory that effective stabilizing agents act by favoring the most compact structure of a protein, thereby reducing local backbone fluctuations away from the fully folded state. Such inhibition of protein backbone dynamics may be a general mechanism of protein stabilization in extreme thermal or chemical environments. PMID:8718847

  7. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity

    PubMed Central

    Moccia, Maria; Adamo, Mauro F A; Saviano, Michele

    2014-01-01

    PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed. PMID:26752710

  8. Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

    ERIC Educational Resources Information Center

    Jerome, Brian; Fuqua, Paul

    This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

  9. Oligonucleotides with conjugated dihydropyrroloindole tripeptides: base composition and backbone effects on hybridization.

    PubMed Central

    Kutyavin, I V; Lukhtanov, E A; Gamper, H B; Meyer, R B

    1997-01-01

    The ability of conjugated minor groove binding (MGB) residues to stabilize nucleic acid duplexes was investigated by synthesis of oligonucleotides bearing a tethered dihydropyrroloindole tripeptide (CDPI3). Duplexes bearing one or more of these conjugated MGBs were varied by base composition (AT- or GC-rich oligonucleotides), backbone modifications (phosphodiester DNA, 2'-O-methyl phosphodiester RNA or phosphorothioate DNA) and site of attachment of the MGB moiety (5'- or 3'-end of either duplex strand). Melting temperatures of the duplexes were determined. The conjugated CDPI3 residue enhanced the stability of virtually all duplexes studied. The extent of stabilization was backbone and sequence dependent and reached a maximum value of 40-49 degrees C for d(pT)8. d(pA)8. Duplexes with a phosphorothioate DNA backbone responded similarly on CDPI3 conjugation, although they were less stable than analogous phosphodiesters. Modest stabilization was obtained for duplexes with a 2'-O-methyl RNA backbone. The conjugated CDPI3 residue stabilized GC-rich DNA duplexes, albeit to a lesser extent than for AT-rich duplexes of the same length. PMID:9278496

  10. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments

    PubMed Central

    Hotchko, Matthew; Anand, Ganesh S.; Komives, Elizabeth A.; Ten Eyck, Lynn F.

    2006-01-01

    A Fourier deconvolution method has been developed to explicitly determine the amount of backbone amide deuterium incorporated into protein regions or segments by hydrogen/deuterium (H/D) exchange with high-resolution mass spectrometry. Determination and analysis of the level and number of backbone amide exchanging in solution provide more information about the solvent accessibility of the protein than do previous centroid methods, which only calculate the average deuterons exchanged. After exchange, a protein is digested into peptides as a way of determining the exchange within a local area of the protein. The mass of a peptide upon deuteration is a sum of the natural isotope abundance, fast exchanging side-chain hydrogens (present in MALDI-TOF H/2H data) and backbone amide exchange. Removal of the components of the isotopic distribution due to the natural isotope abundances and the fast exchanging side-chains allows for a precise quantification of the levels of backbone amide exchange, as is shown by an example from protein kinase A. The deconvoluted results are affected by overlapping peptides or inconsistent mass envelopes, and evaluation procedures for these cases are discussed. Finally, a method for determining the back exchange corrected populations is presented, and its effect on the data is discussed under various circumstances. PMID:16501228

  11. On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

    PubMed

    Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

    2015-05-01

    Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements.

  12. Linear discrete diffraction and transverse localization of light in two-dimensional backbone lattices.

    PubMed

    Qi, Yiling; Zhang, Guoquan

    2010-09-13

    We study the linear discrete diffraction characteristics of light in two-dimensional backbone lattices. It is found that, as the refractive index modulation depth of the backbone lattice increases, high-order band gaps become open and broad in sequence, and the allowed band curves of the Floquet-Bloch modes become flat gradually. As a result, the diffraction pattern at the exit face converges gradually for both the on-site and off-site excitation cases. Particularly, when the refractive index modulation depth of the backbone lattice is high enough, for example, on the order of 0.01 for a square lattice, the light wave propagating in the backbone lattice will be localized in transverse dimension for both the on-site and off-site excitation cases. This is because only the first several allowed bands with nearly flat band curves are excited in the lattice, and the transverse expansion velocities of the Floquet-Bloch modes in these flat allowed bands approach to zero. Such a linear transverse localization of light may have potential applications in navigating light propagation dynamics and optical signal processing.

  13. Peptide-functionalized semiconductor surfaces: strong surface electronic effects from minor alterations to backbone composition.

    PubMed

    Matmor, Maayan; Lengyel, George A; Horne, W Seth; Ashkenasy, Nurit

    2017-02-22

    The use of non-canonical amino acids is a powerful way to control protein structure. Here, we show that subtle changes to backbone composition affect the ability of a dipeptide to modify solid surface electronic properties. The extreme sensitivity of the interactions to the peptide structure suggests potential applications in improving the performance of electronic devices.

  14. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

    PubMed Central

    Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

    2013-01-01

    We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

  15. A backbone design principle for covalent organic frameworks: the impact of weakly interacting units on CO2 adsorption.

    PubMed

    Zhai, Lipeng; Huang, Ning; Xu, Hong; Chen, Qiuhong; Jiang, Donglin

    2017-03-31

    Covalent organic frameworks are designed to have backbones with different yet discrete contents of triarylamine units that interact weakly with CO2. Adsorption experiments indicate that the triarylamine units dominate the CO2 adsorption process and the CO2 uptake increases monotonically with the triarylamine content. These profound collective effects reveal a principle for designing backbones targeting for CO2 capture and separation.

  16. Fc-optimized NKG2D-Fc constructs induce NK cell antibody-dependent cellular cytotoxicity against breast cancer cells independently of HER2/neu expression status.

    PubMed

    Raab, Stefanie; Steinbacher, Julia; Schmiedel, Benjamin J; Kousis, Philaretos C; Steinle, Alexander; Jung, Gundram; Grosse-Hovest, Ludger; Salih, Helmut R

    2014-10-15

    The ability of NK cells to mediate Ab-dependent cellular cytotoxicity (ADCC) largely contributes to the clinical success of antitumor Abs, including trastuzumab, which is approved for the treatment of breast cancer with HER2/neu overexpression. Notably, only ∼25% of breast cancer patients overexpress HER2/neu. Moreover, HER2/neu is expressed on healthy cells, and trastuzumab application is associated with side effects. In contrast, the ligands of the activating immunoreceptor NKG2D (NKG2DL) are selectively expressed on malignant cells. In this study, we took advantage of the tumor-associated expression of NKG2DL by using them as target Ags for NKG2D-IgG1 fusion proteins optimized by amino acid exchange S239D/I332E in their Fc part. Compared to constructs with wild-type Fc parts, fusion proteins carrying the S239D/I332E modification (NKG2D-Fc-ADCC) mediated highly enhanced degranulation, ADCC, and IFN-γ production of NK cells in response to breast cancer cells. NKG2D-Fc-ADCC substantially enhanced NK reactivity also against HER2/neu-low targets that were unaffected by trastuzumab, as both compounds mediated their immunostimulatory effects in strict dependence of target Ag expression levels. Thus, in line with the hierarchically organized potential of the various activating receptors governing NK reactivity and due to its highly increased affinity to CD16, NKG2D-Fc-ADCC potently enhances NK cell reactivity despite the inevitable reduction of activating signals upon binding to NKG2DL. Due to the tumor-restricted expression of NKG2DL, NKG2D-Fc-ADCC may constitute an attractive means for immunotherapy especially of HER2/neu-low or -negative breast cancer.

  17. Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics.

    PubMed

    Buchko, Garry W; Perkins, Arden; Parsonage, Derek; Poole, Leslie B; Karplus, P Andrew

    2016-04-01

    Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond.

  18. Backbone dynamics measurements on leukemia inhibitory factor, a rigid four-helical bundle cytokine.

    PubMed Central

    Yao, S.; Smith, D. K.; Hinds, M. G.; Zhang, J. G.; Nicola, N. A.; Norton, R. S.

    2000-01-01

    The backbone dynamics of the four-helical bundle cytokine leukemia inhibitory factor (LIF) have been investigated using 15N NMR relaxation and amide proton exchange measurements on a murine-human chimera, MH35-LIF. For rapid backbone motions (on a time scale of 10 ps to 100 ns), as probed by 15N relaxation measurements, the dynamics parameters were calculated using the model-free formalism incorporating the model selection approach. The principal components of the inertia tensor of MH35-LIF, as calculated from its NMR structure, were 1:0.98:0.38. The global rotational motion of the molecule was, therefore, assumed to be axially symmetric in the analysis of its relaxation data. This yielded a diffusion anisotropy D(parallel)/D(perpendicular) of 1.31 and an effective correlation time (4D(perpendicular) + 2D(parallel))(-1) of 8.9 ns. The average values of the order parameters (S2) for the four helices, the long interhelical loops, and the N-terminus were 0.91, 0.84, and 0.65, respectively, indicating that LIF is fairly rigid in solution, except at the N-terminus. The S2 values for the long interhelical loops of MH35-LIF were higher than those of their counterparts in short-chain members of the four-helical bundle cytokine family. Residues involved in LIF receptor binding showed no consistent pattern of backbone mobilities, with S2 values ranging from 0.71 to 0.95, but residues contributing to receptor binding site III had relatively lower S2 values, implying higher amplitude motions than for the backbone of sites I and II. In the relatively slow motion regime, backbone amide exchange measurements showed that a number of amides from the helical bundle exchanged extremely slowly, persisting for several months in 2H2O at 37 degrees C. Evidence for local unfolding was considered, and correlations among various structure-related parameters and the backbone amide exchange rates were examined. Both sets of data concur in showing that LIF is one of the most rigid four

  19. SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

    PubMed Central

    Maupetit, Julien; Gautier, R.; Tufféry, Pierre

    2006-01-01

    SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at . PMID:16844979

  20. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    PubMed

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  1. How Sensitive Is the Amide I Vibration of the Polypeptide Backbone to Electric Field?

    PubMed Central

    Oh, Kwang-Im; Fiorin, Giacomo

    2015-01-01

    Site-selective isotopic labelling of amide carbonyls offers a non-perturbative means to introduce a localized infrared probe into proteins. While this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric field (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α-helix is determined to be approximately 1.4 cm−1/(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant. PMID:26419214

  2. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    PubMed Central

    Shen, Yang; Bax, Ad

    2013-01-01

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

  3. Design of an all-fiber erbium-doped laser system for simulating power load in backbone networks

    NASA Astrophysics Data System (ADS)

    Pobořil, Radek; Bednárek, Lukáš; Vanderka, Aleš; Hájek, Lukáš; Zbořil, Ondřej; Vašinek, Vladimír

    2016-12-01

    This article is focused on the design of an all-fiber laser that was supposed to be used for simulating power load similar to the power load in backbone networks. The first part of the article is a brief introduction to the topic of lasers and erbium doped fiber amplifiers. The following parts present design of a fiber laser with ring cavity, and measuring the ideal length of a doped fiber and the split ratio of the output coupler. After proposing the first stage -a laser- we focused on the construction of the two following stages -EDFA preamplifier and EDFA amplifier. There were used fibers with various levels of erbium ion density, namely ISO-GAIN I6, and Liekki ER110-4/125. The resulting output power of the whole system was 320 mW. This value is sufficient when we take into account that we used only single-mode fibers with energy pumped directly to the fiber core. The output wavelength of the whole laser system was 1559 nm.

  4. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, George A.; Nelson, David A.; Molton, Peter M.

    1992-01-01

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

  5. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, G.A.; Nelson, D.A.; Molton, P.M.

    1992-03-31

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

  6. Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

    PubMed

    Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-04-07

    Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

  7. Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

    PubMed

    Davey, James A; Chica, Roberto A

    2014-05-01

    Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability.

  8. Hash: a Program to Accurately Predict Protein Hα Shifts from Neighboring Backbone Shifts3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2012-01-01

    Chemical shifts provide not only peak identities for analyzing NMR data, but also an important source of conformational information for studying protein structures. Current structural studies requiring Hα chemical shifts suffer from the following limitations. (1) For large proteins, the Hα chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of Cα that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict Hα chemical shifts. Predicting accurate Hα chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict Hα chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate Hα chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins. PMID:23242797

  9. Effect of protein backbone folding on the stability of protein-ligand complexes.

    PubMed

    Estrada, Ernesto; Uriarte, Eugenio; Vilar, Santiago

    2006-01-01

    The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding of the protein S correlates in a significant way with the free energy and enthalpy of the protein-peptide interactions. A much better correlation is found with the local contribution to the degree of folding of one amino acid residue: Thr36. This residue is shown to have a destabilizing interaction with Lys41, which interacts directly with peptide S. Another system, consisting of the interactions of small organic molecules with HIV-1 protease was also studied. In this case, the global change in the degree of folding of the protease backbone does not explain the binding energetics of protein-ligand interactions. However, a significant correlation is observed between the free energy of binding and the contribution of two amino acid residues in the HVI-1 protease: Gly49 and Ile66. In general, it was observed that the changes in the degree of folding are not restricted to the binding site of the protein chain but are distributed along the whole protein backbone. This study provides a basis for further consideration of the degree of folding as a parameter for empirical structural parametrizations of the binding energetics of protein folding and binding.

  10. Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase

    PubMed Central

    Harris, Karen S.; Durek, Thomas; Kaas, Quentin; Poth, Aaron G.; Gilding, Edward K.; Conlan, Brendon F.; Saska, Ivana; Daly, Norelle L.; van der Weerden, Nicole L.; Craik, David J.; Anderson, Marilyn A.

    2015-01-01

    Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identification of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia affinis. We recombinantly express OaAEP1b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1b cannot cleave at the N-terminal site of O. affinis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired. PMID:26680698

  11. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

    PubMed

    Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-10-14

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

  12. Androgen deprivation therapy as backbone therapy in the management of prostate cancer

    PubMed Central

    Merseburger, Axel S; Alcaraz, Antonio; von Klot, Christoph A

    2016-01-01

    Androgen deprivation therapy (ADT) is well established as a backbone therapy for metastatic prostate cancer (mPCa), and both European and American guidelines emphasize the importance of maintaining ADT after progression to metastatic castration-resistant prostate cancer (CRPC). However, the use of ADT varies widely in clinical practice despite these recommendations. Both research and development of increasingly precise assay technologies have improved our understanding of androgen production and signaling, and the recent data have suggested that a new serum testosterone cutoff value of <0.7 nmol/L should be employed. Most clinical trials to date have used the historical 1.7 nmol/L cutoff, but the <0.7 nmol/L cutoff has been associated with improved patient outcomes. Combining agents with different mechanisms of action to achieve intense androgen blockade may improve survival both before and after progression to CRPC. Data suggest that this intensive approach to androgen deprivation could delay the transition to CPRC and hence improve survival dramatically. Various combinations of backbone ADT with chemotherapy or radiotherapy are under investigation. Administration of ADT is established in patients with intermediate or high-risk localized prostate cancer (PCa) receiving radiotherapy with curative intent. This article reviews the current and potential role of ADT as backbone therapy in both hormone-sensitive PCa and CRPC with a focus on mPCa. PMID:27942220

  13. East vergent structure of Backbone Range: Insights from A-Lan-Yi area and sandbox modeling

    NASA Astrophysics Data System (ADS)

    Lee, C. A.; Lu, C. Y.

    2015-12-01

    Southern Taiwan, including Pingtung peninsula and Taitung, is the incipient oblique collision zone of Eurasian plate and Philippine Sea plate. The Luzon volcanic arc converged toward Taiwan Island and formed Hengchun Ridge south offshore Taiwan. Thus, Taiwan mountain belt developed from north to south as the Backbone Range, so that we can infer the incipient feature structure from the topography and outcrop study of southern Taiwan. Our field survey of this study concentrated at the southeast coastline of Taiwan, also known as A-Lan-Yi Trail. According to previous study, the deformational structures such as faults and folds are consistent with regional kinematic processes, and the preserved transpression structure is the most important evidence of incipient collision. In this study, we use the sedimentary sequences of study area to trace the regional tectonics from north to south. Discovered structures in this area show the similar kinematic history as the eastern flank of Backbone Range, so that we suggest they are at the same series of a tectonic event. To complete the regional structure mapping in this accessible area, besides the field geological data, we also applied the LiDAR-derived DTM which is a 3D visualization technology to improve our topography information. In addition, we use the sandbox modeling to demonstrate the development of structures in the eastern flank of Backbone Range. After combining the results of field observation and regional structure mapping, this study provides a strong evidence of backthrusting and backfolding deformation during the incipient oblique collision stage.

  14. No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

    PubMed

    Hu, Hao; Ziff, Robert M; Deng, Youjin

    2016-10-28

    The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

  15. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

    PubMed Central

    Riml, Christian; Glasner, Heidelinde; Rodgers, M. T.; Micura, Ronald; Breuker, Kathrin

    2015-01-01

    Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M−nH)n− ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage. PMID:25904631

  16. Synthesis and structural characterization of one- and two-dimensional coordination polymers based on platinum-silver metallic backbones.

    PubMed

    Liu, Fenghui; Chen, Wanzhi; Wang, Daqi

    2006-06-28

    Seven Pt-Ag coordination polymers [Pt(NH3)2(NHCO(t)Bu)2Ag(H2O)](ClO4) (1), [Pt2(dap)2(NHCO(t)Bu)4Ag2(NO3)(ClO4)] (dap = 1,2-diaminopropane, 2), [Pt2(en)2(NHCO(t)Bu)4Ag2(m-C6H4(CO2)2)].3H2O (en = ethylenediamine, 3), [Pt2(NH3)2(NHCO(t)Bu)2Ag2(p-C6H4(CO2)2)].2H2O (4), [Pt3(en)3(NHCO(t)Bu)6Ag2(p-C6H4(CO2)2)(1.5)].6H2O (5), [Pt(NH3)2(NHCO(t)Bu)4Ag(4-C5H4NCO2)2].10H2O (6), and [Pt2(en)2(NHCO(t)Bu)4Ag2(4-C5H4NCO2)](ClO4) (7) were synthesized from the corresponding [Pt(RNH2)2(NHCO(t)Bu)2] and Ag salts, respectively, and their structures were determined by X-ray crystallography. The Pt and Ag units aggregate into one-dimensional chains based on Pt-Ag backbones. Compounds 1, 2, and 6 possess an extended zigzag Pt-Ag chain motif, and the metallic chains arrange in a parallel fashion into layered structures. Compounds 3-5, and 7 form 2-D brick wall sheets due to the coordination of the bifunctional anions to the Ag+ ions of the neighboring chains. These polymers are constructed based on the Pt-Ag interactions and the coordination of amidate oxygen atoms to Ag ions. There are three kinds of short Pt-Ag bonds observed in the structures of these compounds. The Pt-Ag metallic backbone is formed by the stacking unsupported Pt-Ag bonds, the amidate doubly bridged Pt-Ag bonds, and the amidate singly bridged Pt-Ag bonds. In the chains, the Pt-Ag bond distances are quite short, and appear in the range of 2.78-2.97 A, which are comparable to known Pt-Ag dative bonds.

  17. Broadly Neutralizing Anti-Influenza Virus Antibodies: Enhancement of Neutralizing Potency in Polyclonal Mixtures and IgA Backbones

    PubMed Central

    He, Wenqian; Mullarkey, Caitlin E.; Duty, J. Andrew; Moran, Thomas M.; Palese, Peter

    2015-01-01

    ABSTRACT Current influenza virus vaccines rely upon the accurate prediction of circulating virus strains months in advance of the actual influenza season in order to allow time for vaccine manufacture. Unfortunately, mismatches occur frequently, and even when perfect matches are achieved, suboptimal vaccine efficacy leaves several high-risk populations vulnerable to infection. However, the recent discovery of broadly neutralizing antibodies that target the hemagglutinin (HA) stalk domain has renewed hope that the development of “universal” influenza virus vaccines may be within reach. Here, we examine the functions of influenza A virus hemagglutinin stalk-binding antibodies in an endogenous setting, i.e., as polyclonal preparations isolated from human sera. Relative to monoclonal antibodies that bind to the HA head domain, the neutralization potency of monoclonal stalk-binding antibodies was vastly inferior in vitro but was enhanced by several orders of magnitude in the polyclonal context. Furthermore, we demonstrated a surprising enhancement in IgA-mediated HA stalk neutralization relative to that achieved by antibodies of IgG isotypes. Mechanistically, this could be explained in two ways. Identical variable regions consistently neutralized virus more potently when in an IgA backbone compared to an IgG backbone. In addition, HA-specific memory B cells isolated from human peripheral blood were more likely to be stalk specific when secreting antibodies of IgA isotypes compared to those secreting IgG. Taken together, our data provide strong evidence that HA stalk-binding antibodies perform optimally when in a polyclonal context and that the targeted elicitation of HA stalk-specific IgA should be an important consideration during “universal” influenza virus vaccine design. IMPORTANCE Influenza viruses remain one of the most worrisome global public health threats due to their capacity to cause pandemics. While seasonal vaccines fail to protect against the

  18. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

    PubMed

    Faller, Christina E; Guvench, Olgun

    2015-05-21

    Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information

  19. Inorganic backbone ionomers: Design and dielectric response of single-ion conducting polymers

    NASA Astrophysics Data System (ADS)

    Bartels, Joshua

    Ion-conducting polymers were studied primarily through the use of dielectric spectroscopy. The conclusions drawn from ion conduction models of the dielectric data are corroborated by additional independent experiments, including x-ray scattering, calorimetry, prism coupling, and DFT calculations. The broad concern of this dissertation is to understand and clarify a path forward in ion conducting polymer research. This is achieved by considering low-Tg ionomers and the advantages imparted by siloxane and phosphazene backbones. The most successful dielectric spectroscopy model for the materials studied is the electrode polarization model (EP), whereas other models, such as the Dyre random barrier model, fail to describe the experimental results. Seven nonionic ether oxygen (EO) containing polymers were studied in order to observe the effect that backbone chemistry has on dipole motion. Conventional carboncarbon backbone EO-containing polymers show no distinct advantage over similar EO-pendant polysiloxane or polyphosphazene systems. The mobility and effective backbone Tg imparted by the inorganic backbones are comparable. A short EO pendant results in a lower static dielectric constant due to restricted motion of dipoles close to the chain. The flexibility and chemical versatility of inorganic backbone polymers motivates further study of two ionomer systems. A polypohosphazene iodide conducting system was characterized by dielectric spectroscopy and x-ray scattering. Two end "tail" functionalization of the ammonium ion were used, a tail with two EOs and an alkyl tail of six carbons. This functional group plays an important role in ion dynamics and can wrap around the ion and self-solvate when EOs are present. The iodide-ammonium ionomers are observed to have unusually large high-frequency dielectric constants due to atomic polarization of ions. The strength of the atomic polarization scales with ion content. The aggregation state of ions is able to be determined from

  20. Chiral counteranion synergistic organocatalysis under high temperature: efficient construction of optically pure spiro[cyclohexanone-oxindole] backbone.

    PubMed

    Lan, Yu-Bao; Zhao, Hua; Liu, Zhao-Min; Liu, Guo-Gui; Tao, Jing-Chao; Wang, Xing-Wang

    2011-09-16

    The combination of a cinchona-based chiral primary amine and a BINOL-phosphoric acid has been demonstrated as a powerful and synergistic catalyst system for the double Michael addition of isatylidene malononitriles with α,β-unsaturated ketones, to provide the novel chiral spiro [cyclohexane-1,3'-indoline]-2',3-diones in high yields (88-99%) with excellent diastereo- and enantioselectivities (94:6-99:1 dr's, 95-99% ee's).

  1. Analytic Models of Oxygen and Nutrient Diffusion, Metabolism Dynamics, and Architecture Optimization in Three-Dimensional Tissue Constructs with Applications and Insights in Cerebral Organoids

    PubMed Central

    2016-01-01

    Diffusion models are important in tissue engineering as they enable an understanding of gas, nutrient, and signaling molecule delivery to cells in cell cultures and tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically applicable, it will be essential to understand internal dynamics and signaling molecule concentrations throughout the tissue and whether cells are receiving appropriate nutrient delivery. Diffusion characteristics present a significant limitation in many engineered tissues, particularly for avascular tissues and for cells whose viability, differentiation, or function are affected by concentrations of oxygen and nutrients. This article seeks to provide novel analytic solutions for certain cases of steady-state and nonsteady-state diffusion and metabolism in basic 3D construct designs (planar, cylindrical, and spherical forms), solutions that would otherwise require mathematical approximations achieved through numerical methods. This model is applied to cerebral organoids, where it is shown that limitations in diffusion and organoid size can be partially overcome by localizing metabolically active cells to an outer layer in a sphere, a regionalization process that is known to occur through neuroglial precursor migration both in organoids and in early brain development. The given prototypical solutions include a review of metabolic information for many cell types and can be broadly applied to many forms of tissue constructs. This work enables researchers to model oxygen and nutrient delivery to cells, predict cell viability, study dynamics of mass transport in 3D tissue constructs, design constructs with improved diffusion capabilities, and accurately control molecular concentrations in tissue constructs that may be used in studying models of development and disease or for conditioning cells to enhance survival after insults like ischemia or implantation into the body, thereby providing a

  2. Effect of Liquid-Crystalline Epoxy Backbone Structure on Thermal Conductivity of Epoxy-Alumina Composites

    NASA Astrophysics Data System (ADS)

    Giang, Thanhkieu; Kim, Jinhwan

    2017-01-01

    In a series of papers published recently, we clearly demonstrated that the most important factor governing the thermal conductivity of epoxy-Al2O3 composites is the backbone structure of the epoxy. In this study, three more epoxies based on diglycidyl ester-terminated liquid-crystalline epoxy (LCE) have been synthesized to draw conclusions regarding the effect of the epoxy backbone structure on the thermal conductivity of epoxy-alumina composites. The synthesized structures were characterized by proton nuclear magnetic resonance (1H-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. Differential scanning calorimetry, thermogravimetric analysis, and optical microscopy were also employed to examine the thermal and optical properties of the synthesized LCEs and the cured composites. All three LCE resins exhibited typical liquid-crystalline behaviors: clear solid crystalline state below the melting temperature ( T m), sharp crystalline melting at T m, and transition to nematic phase above T m with consequent isotropic phase above the isotropic temperature ( T i). The LCE resins displayed distinct nematic liquid-crystalline phase over a wide temperature range and retained liquid-crystalline phase after curing, with high thermal conductivity of the resulting composite. The thermal conductivity values ranged from 3.09 W/m-K to 3.89 W/m-K for LCE-Al2O3 composites with 50 vol.% filler loading. The steric effect played a governing role in the difference. The neat epoxy resin thermal conductivity was obtained as 0.35 W/m-K to 0.49 W/m-K based on analysis using the Agari-Uno model. The results clearly support the objective of this study in that the thermal conductivity of the LCE-containing networks strongly depended on the epoxy backbone structure and the degree of ordering in the cured network.

  3. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    PubMed

    Keedy, Daniel A; Fraser, James S; van den Bedem, Henry

    2015-10-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  4. Membrane Curvature Sensing by Amphipathic Helices Is Modulated by the Surrounding Protein Backbone

    PubMed Central

    Doucet, Christine M.; Esmery, Nina; de Saint-Jean, Maud; Antonny, Bruno

    2015-01-01

    Membrane curvature is involved in numerous biological pathways like vesicle trafficking, endocytosis or nuclear pore complex assembly. In addition to its topological role, membrane curvature is sensed by specific proteins, enabling the coordination of biological processes in space and time. Amongst membrane curvature sensors are the ALPS (Amphipathic Lipid Packing Sensors). ALPS motifs are short peptides with peculiar amphipathic properties. They are found in proteins targeted to distinct curved membranes, mostly in the early secretory pathway. For instance, the ALPS motif of the golgin GMAP210 binds trafficking vesicles, while the ALPS motif of Nup133 targets nuclear pores. It is not clear if, besides curvature sensitivity, ALPS motifs also provide target specificity, or if other domains in the surrounding protein backbone are involved. To elucidate this aspect, we studied the subcellular localization of ALPS motifs outside their natural protein context. The ALPS motifs of GMAP210 or Nup133 were grafted on artificial fluorescent probes. Importantly, ALPS motifs are held in different positions and these contrasting architectures were mimicked by the fluorescent probes. The resulting chimeras recapitulated the original proteins localization, indicating that ALPS motifs are sufficient to specifically localize proteins. Modulating the electrostatic or hydrophobic content of Nup133 ALPS motif modified its avidity for cellular membranes but did not change its organelle targeting properties. In contrast, the structure of the backbone surrounding the helix strongly influenced targeting. In particular, introducing an artificial coiled-coil between ALPS and the fluorescent protein increased membrane curvature sensitivity. This coiled-coil domain also provided membrane curvature sensitivity to the amphipathic helix of Sar1. The degree of curvature sensitivity within the coiled-coil context remains correlated to the natural curvature sensitivity of the helices. This suggests

  5. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    SciTech Connect

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  6. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    DOE PAGES

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; ...

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechainmore » conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

  7. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

    PubMed Central

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry

    2015-01-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems. PMID:26506617

  8. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation.

    PubMed

    Qvit, Nir; Kornfeld, Opher S

    2016-01-26

    Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a

  9. Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

    PubMed

    Vögeli, Beat; Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2007-08-01

    3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' couplings, all related to the backbone torsion angle phi, were measured for the third immunoglobulin binding domain of protein G, or GB3. Measurements were carried out using both previously published methods and novel sequences based on the multiple-quantum principle, which limit attenuation of experimental couplings caused by finite lifetimes of the spin states of passive spins. High reproducibility between the multiple-quantum and conventional approaches confirms the accuracy of the measurements. With few exceptions, close agreement between 3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' and values predicted by their respective Karplus equations is observed. For the three types of couplings, up to 20% better agreement is obtained when fitting the experimental couplings to a dynamic ensemble NMR structure, which has a phi angle root-mean-square spread of 9 +/- 4 degrees and was previously calculated on the basis of a very extensive set of residual dipolar couplings, than for any single static NMR structure. Fits of 3J couplings to a 1.1-A X-ray structure, with hydrogens added in idealized positions, are 40-90% worse. Approximately half of the improvement when fitting to the NMR structures relates to the amide proton deviating from its idealized, in-peptide-plane position, indicating that the positioning of hydrogens relative to the backbone atoms is one of the factors limiting the accuracy at which the backbone torsion angle phi can be extracted from 3J couplings. Introducing an additional, residue-specific variable for the amplitude of phi angle fluctuations does not yield a statistically significant improvement when fitting to a set of dynamic Karplus curves, pointing to a homogeneous behavior of these amplitudes.

  10. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    PubMed Central

    2011-01-01

    Background The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin. PMID:21635747

  11. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https

  12. Graphene-network-backboned architectures for high-performance lithium storage.

    PubMed

    Gong, Yongji; Yang, Shubin; Liu, Zheng; Ma, Lulu; Vajtai, Robert; Ajayan, Pulickel M

    2013-08-07

    An efficient hydrothermal approach is demonstrated to fabricate a series of graphene-network-backboned hybrid architectures such as MoS₂/graphene and FeOx/graphene, showing high specific surface area, porous structure, and continuous graphene networks. Such unique architectures exhibit a high reversible capacity (about 1100 mA h g⁻¹) for lithium ion batteries. High-rate capabilities of full charge to discharge in 25-45 s with a long cycle life (1500 cycles) are achieved at different rates.

  13. Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses.

    PubMed

    Russell, Charles J; Hurwitz, Julia L

    2016-01-01

    Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses, including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4) and human metapneumovirus (hMPV), are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV and other hPIV vaccines for children.

  14. Localization of strain in the RNA backbone and its functional implication

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Rabitz, Herschel

    1992-07-01

    It is known that an RNA molecule capable of self-splicing shares a common pattern of Watson-Crick base paris with other RNA species endowed with the same capability. The aim of this work is to introduce a minimal model Hamiltonian which determines a localized strain in the RNA backbone as the search for the molecular conformation is subject to the constraint imposed by the concensus secondary structure. The site where the strain is localized is shown to coincide with the splicing site of the molecule. As justified posteriori, the level of structural complexity of the model is sufficient to account for energy localization in a nontrivial fashion.

  15. Colloidal quantum dot lasers built on a passive two-dimensional photonic crystal backbone.

    PubMed

    Chang, Hojun; Min, Kyungtaek; Lee, Myungjae; Kang, Minsu; Park, Yeonsang; Cho, Kyung-Sang; Roh, Young-Geun; Hwang, Sung Woo; Jeon, Heonsu

    2016-03-28

    We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable.

  16. An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain

    NASA Technical Reports Server (NTRS)

    Luo, N.; Shibata, M.; Rein, R.

    1991-01-01

    A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone. An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed. The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.

  17. Backbone resonance assignments of the micro-RNA precursor binding region of human TRBP.

    PubMed

    Benoit, Matthieu P M H; Plevin, Michael J

    2013-10-01

    TAR-RNA binding protein (TRBP) is a multidomain human protein involved in micro-RNA (miRNA) biogenesis. TRBP is a component of both the Dicer complex, which processes precursor miRNAs, and the RNA-induced silencing complex-loading complex. In addition, TRBP is implicated in the human immunodeficiency virus replication cycle and interferon-protein kinase R activity. TRBP contains 3 double-stranded RNA binding domains the first two of which have been shown to interact with miRNA precursors. Here we present the backbone resonance assignments and secondary structure of residues 19-228 of human TRBP2.

  18. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    SciTech Connect

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; Berg, Volker; Cabelli, Diane E.; Maroney, Michael J.

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz

  19. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development

    PubMed Central

    Mott, Tiffany M.; Vijayakumar, Sudhamathi; Sbrana, Elena; Endsley, Janice J.; Torres, Alfredo G.

    2015-01-01

    Background In this study, a Burkholderia mallei tonB mutant (TMM001) deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis. Methodology/Principal Findings Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 104 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001. Conclusions/Significance Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis. PMID:26114445

  20. A semisynthetic strategy leads to alteration of the backbone amidate ligand in the NiSOD active site

    DOE PAGES

    Campeciño, Julius O.; Dudycz, Lech W.; Tumelty, David; ...

    2015-07-01

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, NΔ5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategymore » that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ~1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ~11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. 14N-hyperfine is observed on gz« less

  1. Low Molecular Weight Oligomers with Aromatic Backbone as Efficient Nonviral Gene Vectors.

    PubMed

    Luan, Chao-Ran; Liu, Yan-Hong; Zhang, Ji; Yu, Qing-Ying; Huang, Zheng; Wang, Bing; Yu, Xiao-Qi

    2016-05-04

    A series of oligomers were synthesized via ring-opening polymerization. Although the molecular weights of these oligomers are only ∼2.5 kDa, they could efficiently bind and condense DNA into nanoparticles. These oligomers gave comparable transfection efficiency (TE) to PEI 25 kDa, while their TE could even increase with the presence of serum, and up to 65 times higher TE than PEI was obtained. The excellent serum tolerance was also confirmed by TEM, flow cytometry, and BSA adsorption assay. Moreover, structure-activity relationship studies revealed some interesting factors. First, oligomers containing aromatic rings in the backbone showed better DNA binding ability. These materials could bring more DNA cargo into the cells, leading to much better TE. Second, the isomerism of the disubstituted phenyl group on the oligomer backbone has large effect on the transfection. The ortho-disubstituted ones gave at least 1 order of magnitude higher TE than meta- or para-disubstituted oligomers. Gel electrophoresis involving DNase and heparin indicated that the difficulty to release DNA might contribute to the lower TE of the latter. Such clues may help us to design novel nonviral gene vectors with high efficiency and biocompatibility.

  2. Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

    PubMed Central

    Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

    2016-01-01

    On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications. PMID:27845441

  3. Efficient delivery of RNAi prodrugs containing reversible charge-neutralizing phosphotriester backbone modifications

    PubMed Central

    Meade, Bryan R; Gogoi, Khirud; Hamil, Alexander S; Palm-Apergi, Caroline; van den Berg, Arjen; Hagopian, Jonathan C; Springer, Aaron D; Eguchi, Akiko; Kacsinta, Apollo D; Dowdy, Connor F; Presente, Asaf; Lönn, Peter; Kaulich, Manuel; Yoshioka, Naohisa; Gros, Edwige; Cui, Xian-Shu; Dowdy, Steven F

    2015-01-01

    RNA interference (RNAi) has great potential to treat human disease1–3. However, in vivo delivery of short interfering RNAs (siRNAs), which are negatively charged double-stranded RNA macromolecules, remains a major hurdle4–9. Current siRNA delivery has begun to move away from large lipid and synthetic nanoparticles to more defined molecular conjugates9. Here we address this issue by synthesis of short interfering ribonucleic neutrals (siRNNs) whose phosphate backbone contains neutral phosphotriester groups, allowing for delivery into cells. Once inside cells, siRNNs are converted by cytoplasmic thioesterases into native, charged phosphodiester-backbone siRNAs, which induce robust RNAi responses. siRNNs have favorable drug-like properties, including high synthetic yields, serum stability and absence of innate immune responses. Unlike siRNAs, siRNNs avidly bind serum albumin to positively influence pharmacokinetic properties. Systemic delivery of siRNNs conjugated to a hepatocyte-specific targeting domain induced extended dose-dependent in vivo RNAi responses in mice. We believe that siRNNs represent a technology that will open new avenues for development of RNAi therapeutics. PMID:25402614

  4. NMR Polypeptide Backbone Conformation of the E. coli Outer Membrane Protein W

    PubMed Central

    Horst, Reto; Stanczak, Pawel; Wüthrich, Kurt

    2014-01-01

    SUMMARY The outer membrane proteins (Omp) are key factors for bacterial survival and virulence. Among the Omps which have been structurally characterized either by X-ray crystallography or by NMR in solution, the crystal structure of OmpW stands out because three of its four extracellular loops are well defined, whereas long extracellular loops in other E. coli Omps are disordered in the crystals as well as in NMR structures. OmpW thus presented an opportunity for detailed comparison of the extracellular loops in a β-barrel membrane protein structure in crystals and in non-crystalline milieus. Here the polypeptide backbone conformation of OmpW in 30-Fos micelles was determined. Complete backbone NMR assignments were obtained and the loops were structurally characterized. In combination with the OmpW crystal structure, NMR line shape analyses and 15N{1H}-NOE data, these results showed that intact regular secondary structures in the loops undergo slow hinge motions at the detergent–solvent interface. PMID:25017731

  5. The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin

    PubMed Central

    Castelain, Mickaël; Duviau, Marie-Pierre; Canette, Alexis; Schmitz, Philippe; Loubière, Pascal; Cocaign-Bousquet, Muriel; Piard, Jean-Christophe; Mercier-Bonin, Muriel

    2016-01-01

    Pili produced by Lactococcus lactis subsp. lactis are putative linear structures consisting of repetitive subunits of the major pilin PilB that forms the backbone, pilin PilA situated at the distal end of the pilus, and an anchoring pilin PilC that tethers the pilus to the peptidoglycan. We determined the nanomechanical properties of pili using optical-tweezers force spectroscopy. Single pili were exposed to optical forces that yielded force-versus-extension spectra fitted using the Worm-Like Chain model. Native pili subjected to a force of 0–200 pN exhibit an inextensible, but highly flexible ultrastructure, reflected by their short persistence length. We tested a panel of derived strains to understand the functional role of the different pilins. First, we found that both the major pilin PilB and sortase C organize the backbone into a full-length organelle and dictate the nanomechanical properties of the pili. Second, we found that both PilA tip pilin and PilC anchoring pilin were not essential for the nanomechanical properties of pili. However, PilC maintains the pilus on the bacterial surface and may play a crucial role in the adhesion- and biofilm-forming properties of L. lactis. PMID:27010408

  6. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    SciTech Connect

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2014-06-17

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.

  7. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    DOE PAGES

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; ...

    2014-06-17

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL)more » of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less

  8. Importance of backbone angles versus amino acid configurations in peptide vibrational Raman optical activity spectra

    NASA Astrophysics Data System (ADS)

    Herrmann, Carmen; Ruud, Kenneth; Reiher, Markus

    2008-01-01

    In this work, we investigate whether the differential scattering of right- and left-circularly polarized light in peptide Raman optical activity spectra are uniquely dominated by the backbone conformation, or whether the configurations of the individual amino acid also play a significant role. This is achieved by calculating Raman optical activity spectra using density functional theory for four structurally related peptides with a common backbone conformation, but with different sequences of amino acid configurations. Furthermore, the ROA signals of the amide normal modes are decomposed into contributions from groups of individual atoms. It is found that the amino acid configuration has a considerable influence on the ROA peaks in the amide I, II, and III regions, although the local decomposition reveals that the side-chain atoms only contribute to those peaks directly in the case of the amide II vibrations. Furthermore, small changes in the amide normal modes may lead to large and irregular modifications in the ROA intensity differences, making it difficult to establish transferable ROA intensity differences even for structurally similar vibrations.

  9. Backbone dynamics of the monomeric lambda repressor denatured state ensemble under nondenaturing conditions.

    PubMed

    Chugha, Preeti; Oas, Terrence G

    2007-02-06

    Oxidizing two native methionine residues predominantly populates the denatured state of monomeric lambda repressor (MetO-lambdaLS) under nondenaturing conditions. NMR was used to characterize the secondary structure and dynamics of MetO-lambdaLS in standard phosphate buffer. 13Calpha and 1Halpha chemical shift indices reveal a region of significant helicity between residues 9 and 29. This helical content is further supported by the observation of medium-range amide NOEs. The remaining residues do not exhibit significant helicity as determined by NMR. We determined 15N relaxation parameters for 64 of 85 residues at 600 and 800 MHz. There are two distinct regions of reduced flexibility, residues 8-32 in the N-terminal third and residues 50-83 in the C-terminal third. The middle third, residues 33-50, has greater flexibility. We have analyzed the amplitude of the backbone motions in terms of the physical properties of the amino acids and conclude that conformational restriction of the backbone MetO-lambdaLS is due to nascent helix formation in the region corresponding to native helix 1. The bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions, which is suggested by chemical exchange detected by the difference in spectral density J(0) at the two static magnetic fields. The more flexible middle region is the result of a predominance of small side chains in this region.

  10. Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

    NASA Astrophysics Data System (ADS)

    Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

    2016-11-01

    On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications.

  11. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    PubMed

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  12. Toward Establishing the Validity of the Transformative Optimism Construct Measurement for Tsunami Preparedness: A Structural Equation Model for Visitors of the Pacific Northwest Coast

    ERIC Educational Resources Information Center

    Rios-Uribe, Carlos Andres

    2009-01-01

    Measurements of social constructs that evaluate natural hazard preparedness are important to decrease natural hazard vulnerability. Preparedness reduces natural hazard impacts and human vulnerability. Investment in education and education research contribute to human sustainable development and natural hazard preparedness. Faced with other needs,…

  13. Discovery, adaptation and transcriptional activity of two tick promoters: Construction of a dual luciferase reporter system for optimization of RNA interference in Rhipicephalus (Boophilus) microplus cell lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dual luciferase reporter systems are valuable tools for functional genomic studies, but have not previously been developed for use in tick cell culture. We evaluated expression of available luciferase constructs in tick cell cultures derived from Rhipicephalus (Boophilus) microplus, an important vec...

  14. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    PubMed

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  15. The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

    2015-06-01

    Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

  16. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

    PubMed Central

    Ponomarev, Sergei Y.; Kaminski, George A.

    2011-01-01

    A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:21743799

  17. Sendai Virus as a Backbone for Vaccines against RSV and other Human Paramyxoviruses

    PubMed Central

    Russell, Charles J.; Hurwitz, Julia L.

    2016-01-01

    Summary Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses – including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4), and human metapneumovirus (hMPV) – are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV, and other hPIV vaccines for children. PMID:26648515

  18. Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes

    PubMed Central

    Tae, Hongseok; Settlage, Robert E.; Shallom, Shamira; Bavarva, Jasmin H.; Preston, Dale; Hawkins, Gregory N.; Adams, L. Garry; Garner, Harold R.

    2012-01-01

    Sequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method comprised of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised Brucella suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively. In total, using this iterative approach, we identified on average 87 variants including SNVs, short INDELs and long INDELs per strain when compared to the reference. Our program outperforms other methods especially for long INDEL calling. The program is available at http://reviseq.sourceforge.net. PMID:22967795

  19. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    PubMed

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-01-01

    Dengue fever is caused by infection with one of four dengue virus (DENV) serotypes (DENV-1-4), necessitating tetravalent dengue vaccines that can induce protection against all four DENV. Takeda's live attenuated tetravalent dengue vaccine candidate (TDV) comprises an attenuated DENV-2 strain plus chimeric viruses containing the prM and E genes of DENV-1, -3 and -4 cloned into the attenuated DENV-2 'backbone'. In Phase 1 and 2 studies, TDV was well tolerated by children and adults aged 1.5-45 years, irrespective of prior dengue exposure; mild injection-site symptoms were the most common adverse events. TDV induced neutralizing antibody responses and seroconversion to all four DENV as well as cross-reactive T cell-mediated responses that may be necessary for broad protection against dengue fever.

  20. Modification of Rifamycin Polyketide Backbone Leads to Improved Drug Activity against Rifampicin-resistant Mycobacterium tuberculosis*

    PubMed Central

    Nigam, Aeshna; Almabruk, Khaled H.; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N.; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-01-01

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains. PMID:24923585

  1. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J.

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  2. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    NASA Astrophysics Data System (ADS)

    Sarmento, R. G.; Fulco, U. L.; Albuquerque, E. L.; Caetano, E. W. S.; Freire, V. N.

    2011-10-01

    We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  3. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis.

    PubMed

    Nigam, Aeshna; Almabruk, Khaled H; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-07-25

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains.

  4. Solid-phase synthesis of lidocaine and procainamide analogues using backbone amide linker (BAL) anchoring.

    PubMed

    Shannon, Simon K; Peacock, Mandy J; Kates, Steven A; Barany, George

    2003-01-01

    New solid-phase strategies have been developed for the synthesis of lidocaine (1) and procainamide (2) analogues, using backbone amide linker (BAL) anchoring. Both sets were prepared starting from a common resin-bound intermediate, followed by four general steps: (i) attachment of a primary aliphatic or aromatic amine to the solid support via reductive amination (as monitored by a novel test involving reaction of 2,4-dinitrophenylhydrazine with residual aldehyde groups); (ii) acylation of the resultant secondary amine; (iii) displacement of halide with an amine; and (iv) trifluoroacetic acid-mediated release from the support. A manual parallel strategy was followed to provide 60 novel compounds, of which two dozen have not been previously described. In most cases, initial crude purities were >80%, and overall isolated yields were in the 40-88% range.

  5. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-03-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

  6. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope.

    PubMed

    Hamuro, Yoshitomo

    2017-03-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification. Graphical Abstract ᅟ.

  7. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-01-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

  8. Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP).

    PubMed Central

    Gutiérrez-González, Luis H; Ludwig, Christian; Hohoff, Carsten; Rademacher, Martin; Hanhoff, Thorsten; Rüterjans, Heinz; Spener, Friedrich; Lücke, Christian

    2002-01-01

    Human epidermal-type fatty acid-binding protein (E-FABP) belongs to a family of intracellular 14-15 kDa lipid-binding proteins, whose functions have been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure-function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi-dimensional high-resolution NMR techniques on unlabelled and 15N-enriched recombinant human E-FABP, the 1H and 15N resonance assignments were completed. On the basis of 2008 distance restraints, the three-dimensional solution structure of human E-FABP was subsequently obtained (backbone atom root-mean-square deviation of 0.92+/-0.11 A; where 1 A=0.1 nm), consisting mainly of 10 anti-parallel beta-strands that form a beta-barrel structure. 15N relaxation experiments (T1, T2 and heteronuclear nuclear Overhauser effects) at 500, 600 and 800 MHz provided information on the internal dynamics of the protein backbone. Nearly all non-terminal backbone amide groups showed order parameters S(2)>0.8, with an average value of 0.88+/-0.04, suggesting a uniformly low backbone mobility in the nanosecond-to-picosecond time range. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the beta-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics elaborated in the present study differ markedly from those of the phylogenetically closely related heart-type FABP and the more distantly related ileal lipid-binding protein, implying a strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family. PMID:12049637

  9. Backbone-hydrazone-containing biodegradable copolymeric micelles for anticancer drug delivery

    NASA Astrophysics Data System (ADS)

    Xu, Jing; Luan, Shujuan; Qin, Benkai; Wang, Yingying; Wang, Kai; Qi, Peilan; Song, Shiyong

    2016-11-01

    Well-defined biodegradable, pH-sensitive amphiphilic block polymers, poly(ethylene glycol)-Hyd-poly(lactic acid) (mPEG-Hyd-PLA) which have acid-cleavable linkages in their backbones, were synthesized via ring-opening polymerization initiated from hydrazone-containing macroinitiators. Introducing a hydrazone bond onto the backbone of an amphiphilic copolymer will find a broad-spectrum encapsulation of hydrophobic drugs. Dynamic light scattering (DLS) and transmission electron microscopy showed that the diblock copolymers self-assembled into stable micelles with average diameters of 100 nm. The mean diameters and size distribution of the hydrazone-containing micelles changed obviously in mildly acidic pH (multiple peaks from 1 to 202 nm appeared under a pH 4.0 condition) than in neutral, while there were no changes in the case of non-sensitive ones. Doxorubicin (DOX) and paclitaxel (PTX) were loaded with drug loading content ranging from 2.4 to 3.5 %, respectively. Interestingly, the anticancer drugs released from mPEG-Hyd-PLA micelles could also be promoted by the increased acidity. An in vitro cytotoxicity study showed that the DOX-loaded mPEG-Hyd-PLA micelles have significantly enhanced cytotoxicity against HepG2 cells compared with the non-sensitive poly(ethylene glycol)-block-poly(lactic acid) (mPEG-PLA) micelles. Confocal microscopy observation indicated that more DOX were delivered into the nuclei of cells following 6 or 12 h incubation with DOX-loaded mPEG-Hyd-PLA micelles. In vivo studies on H22-bearing Swiss mice demonstrated the superior anticancer activity of DOX-loaded mPEG-Hyd-PLA micelles over free DOX and DOX-loaded mPEG-PLA micelles. These hydrazone-containing pH-responsive degradable micelles provide a useful strategy for antitumor drug delivery.

  10. Remote consultation and diagnosis in medical imaging using a global PACS backbone network

    NASA Astrophysics Data System (ADS)

    Martinez, Ralph; Sutaria, Bijal N.; Kim, Jinman; Nam, Jiseung

    1993-10-01

    A Global PACS is a national network which interconnects several PACS networks at medical and hospital complexes using a national backbone network. A Global PACS environment enables new and beneficial operations between radiologists and physicians, when they are located in different geographical locations. One operation allows the radiologist to view the same image folder at both Local and Remote sites so that a diagnosis can be performed. The paper describes the user interface, database management, and network communication software which has been developed in the Computer Engineering Research Laboratory and Radiology Research Laboratory. Specifically, a design for a file management system in a distributed environment is presented. In the remote consultation and diagnosis operation, a set of images is requested from the database archive system and sent to the Local and Remote workstation sites on the Global PACS network. Viewing the same images, the radiologists use pointing overlay commands, or frames to point out features on the images. Each workstation transfers these frames, to the other workstation, so that an interactive session for diagnosis takes place. In this phase, we use fixed frames and variable size frames, used to outline an object. The data pockets for these frames traverses the national backbone in real-time. We accomplish this feature by using TCP/IP protocol sockets for communications. The remote consultation and diagnosis operation has been tested in real-time between the University Medical Center and the Bowman Gray School of Medicine at Wake Forest University, over the Internet. In this paper, we show the feasibility of the operation in a Global PACS environment. Future improvements to the system will include real-time voice and interactive compressed video scenarios.

  11. Enhanced biosynthetically directed fractional carbon-13 enrichment of proteins for backbone NMR Assignments

    PubMed Central

    Wenrich, Broc R.; Sonstrom, Reilly E.; Gupta, Riju A.; Rovnyak, David

    2015-01-01

    Routes to carbon-13 enrichment of bacterially expressed proteins include achieving uniform or positionally selective (e.g. ILV-Me, or 13C′, etc.) enrichment. We consider the potential for biosynthetically directed fractional enrichment (e.g. carbon-13 incorporation in the protein less than 100%) for performing routine n-(D)dimensional NMR spectroscopy of proteins. First, we demonstrate an approach to fractional isotope addition where the initial growth media containing natural abundance glucose is replenished at induction with a small amount (e.g. 10%w/w u-13C-glucose) of enriched nutrient. The approach considered here is to add 10% (e.g. 200 mg for a 2 g/L culture) u-13C-glucose at the induction time (OD600=0.8), resulting in a protein with enhanced 13C incorporation that gives almost the same NMR signal levels as an exact 20% 13C sample. Second, whereas fractional enrichment is used for obtaining stereospecific methyl assignments, we find that 13C incorporation levels no greater than 20%w/w yield 13C and 13C-13C spin pair incorporation sufficient to conduct typical 3D-bioNMR backbone experiments on moderate instrumentation (600 MHz, RT probe). Typical 3D-bioNMR experiments of a fractionally enriched protein yield expected backbone connectivities, and did not show amino acid biases in this work, with one exception. When adding 10% u-13C glucose to expression media at induction, there is poor preservation of 13Cα-13Cβ spin pairs in the amino acids ILV, leading to the absence of Cβ signals in HNCACB spectra for ILV, a potentially useful editing effect. Enhanced fractional carbon-13 enrichment provides lower-cost routes to high throughput protein NMR studies, and makes modern protein NMR more cost-accessible. PMID:26256059

  12. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction.

    PubMed

    Amsden, Jason J; Kralj, Joel M; Chieffo, Logan R; Wang, Xihua; Erramilli, Shyamsunder; Spudich, Elena N; Spudich, John L; Ziegler, Lawrence D; Rothschild, Kenneth J

    2007-10-11

    Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.

  13. 40-Gbps optical backbone network deep packet inspection based on FPGA

    NASA Astrophysics Data System (ADS)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

  14. Using gray-based Taguchi method to construct multi-objective optimal model in super-resolution near-field photolithography.

    PubMed

    Yang, Ching-Been; Chiang, Hsiu-Lu

    2013-01-01

    This study integrated thermally induced super-resolution into near-field photolithography and conducted simulation and analysis on line segment fabrication. This technique involves passing a laser beam through an aluminum-plated optical fiber probe onto a thin film of indium (approximately 10 nm thick). The indium film opens a melted aperture narrower than the width of the laser beam, creating a melted region and a crystalline region. The difference in penetration rate between the two regions leads to the generation of thermally induced super-resolution. This paper proposes a combination of Taguchi method with gray relational analysis, in which S/N ratios obtained using the Taguchi method are converted into gray relational grades to identify an optimal combination of parameters capable of meeting multiple quality objectives. This optimal combination includes a probe aperture of 100 nm (A1), exposure energy/μm of 0.002nJ/μm (B2), development time of 60 s (C3), and indium film with a thickness of 7 nm (D1). The optimal parameters were (A1B2C3D1) for the gray relational analysis and (A1B1C1D1) for the Taguchi method. Results showed a negative improvement of -14.3% in line width from 126.2 (Taguchi method) to 144.2 nm (gray relational analysis). Working depth, however, showed a significantly improvement of 140.4% from 5.7 (Taguchi method) to 13.7 nm (gray relational analysis). The proposed approach resolves the conflicts that commonly occur among factor levels in Taguchi analysis under the requirements of multiple quality requirements.

  15. Constructed Wetlands

    EPA Pesticide Factsheets

    these systems can improve water quality, engineers and scientists construct systems that replicate the functions of natural wetlands. Constructed wetlands are treatment systems that use natural processes

  16. Automatised selection of load paths to construct reduced-order models in computational damage micromechanics: from dissipation-driven random selection to Bayesian optimization

    NASA Astrophysics Data System (ADS)

    Goury, Olivier; Amsallem, David; Bordas, Stéphane Pierre Alain; Liu, Wing Kam; Kerfriden, Pierre

    2016-08-01

    In this paper, we present new reliable model order reduction strategies for computational micromechanics. The difficulties rely mainly upon the high dimensionality of the parameter space represented by any load path applied onto the representative volume element. We take special care of the challenge of selecting an exhaustive snapshot set. This is treated by first using a random sampling of energy dissipating load paths and then in a more advanced way using Bayesian optimization associated with an interlocked division of the parameter space. Results show that we can insure the selection of an exhaustive snapshot set from which a reliable reduced-order model can be built.

  17. Optimal design of Ig 5' primers for construction of diverse phage antibody library established to select anti-HAb18GEF and anti-DOTA-Y Fabs for hepatoma pretargeting RIT.

    PubMed

    Zhang, Sihe; Xing, Jinliang; Zhang, Qing; Song, Fei; Li, Yu; Yang, Xiangmin; Chen, Zhinan

    2006-05-01

    Phage antibody library yields antibodies with higher affinity against different antigens, if diverse IgV gene repertoires can be amplified. As the currently available Fab primer sets cannot guarantee efficient amplification with high diversity, and because rare cloning sites can be found in certain Ig genes, here, we present an optimal set of Ig 5' primers, compatible with Fd 5' clone site replaced pComb3 vector, for diverse Fab phage display library construction. These novel Fab primes designed based on the newly classified IgV families, not only have best match and highest coverage for IgV family with minimized N-terminal amino acid changes, but also present good amplification diversity and efficiency of Ig gene from mice immunized with different forms of antigens (HAb18GEF, KLH-DOTA-Y, and HAb18G/pcDNA3). A high quality immune phage library with good diversity was constructed based on the mixed Ig repertoire, and five high affinity Fab antibodies were selected to specifically bind to HAb18GEF, DOTA-Y and an irrelevant antigen gamma-sm, respectively. This novel Fab primers set can be applied to the construction of diverse phage antibody library and the anti-HAb18GEF and anti-DOTA-Y Fab antibodies lay a solid foundation for radioimmunotherapy of hepatoma.

  18. Lunar base construction requirements

    NASA Technical Reports Server (NTRS)

    Jolly, Steve; Helleckson, Brent

    1990-01-01

    The following viewgraph presentation is a review of the Lunar Base Constructibility Study carried out in the spring and summer of 1990. The objective of the study was to develop a method for evaluating the constructibility of Phase A proposals to build facilities on orbit or on extraterrestrial surfaces. Space construction was broadly defined as all forms of assembly, disassembly, connection, disconnection, deployment, stowage, excavation, emplacement, activation, test, transportation, etc., required to create facilities in orbit and on the surfaces of other celestial bodies. It was discovered that decisions made in the face of stated and unstated assumptions early in the design process (commonly called Phase A) can lock in non-optimal construction methods. Often, in order to construct the design, alterations must be made to the design during much later phases of the project. Such 'fixes' can be very difficult, expensive, or perhaps impossible. Assessing constructibility should thus be a part of the iterative design process, starting with the Phase A studies and continuing through production. This study assumes that there exists a minimum set of key construction requirements (i.e., questions whose answers form the set of discriminators) that must be implied or specified in order to assess the constructibility of the design. This set of construction requirements constitutes a 'constructibility filter' which then becomes part of the iterative design process. Five inherently different, dichotomous design reference missions were used in the extraction of these requirements to assure the depth and breath of the list.

  19. Optimization of RNA isolation from Brittle Leaf Disease affected date palm leaves and construction of a subtractive cDNA library.

    PubMed

    Saïdi, Mohammed Najib; Gargouri-Bouzid, Radhia; Rayanni, Mariem; Drira, Noureddine

    2009-01-01

    A simple and efficient method was described here for the isolation of high-quality RNA from date palm leaves affected with Brittle Leaf Disease (BLD) and containing high amount of phenolic compounds. The procedure was based on the use of a non-ionic detergent Nonidet-P40 (NP-40), Polyvinylpyrrolidone (PVP), and beta-mercaptoethanol in the extraction buffer in order to isolate cytoplasmic RNA and to prevent the oxidation of phenolic compounds. This method allowed the isolation of intact RNA, suitable for cDNA synthesis and library construction. Differential screening of the subtractive cDNA library from affected leaf RNA led to the identification of some BLD-induced genes.

  20. Optimization of the Small Glycan Presentation for Binding a Tumor-Associated Antibody: Application to the Construction of an Ultrasensitive Glycan Biosensor.

    PubMed

    Kveton, Filip; Blšáková, Anna; Hushegyi, Andras; Damborsky, Pavel; Blixt, Ola; Jansson, Bo; Tkac, Jan

    2017-03-21

    The main aim of the study was to optimize the interfacial presentation of a small antigen-a Tn antigen (N-acetylgalactosamine)-for binding to its analyte anti-Tn antibody. Three different methods for the interfacial display of a small glycan are compared here, including two methods based on the immobilization of the Tn antigen on a mixed self-assembled monolayer (SAM) (2D biosensor) and the third one utilizing a layer of a human serum albumin (HSA) for the immobilization of a glycan forming a 3D interface. Results showed that the 3D interface with the immobilized Tn antigen is the most effective bioreceptive surface for binding its analyte. The 3D impedimetric glycan biosensor exhibited a limit of detection of 1.4 aM, a wide linear range (6 orders of magnitude), and high assay reproducibility with an average relative standard deviation of 4%. The buildup of an interface was optimized using various techniques with the visualization of the glycans on the biosensor surface by atomic force microscopy. The study showed that the 3D biosensor is not only the most sensitive compared to other two biosensor platforms but that the Tn antigen on the 3D biosensor surface is more accessible for antibody binding with better kinetics of binding (t50% = 137 s, t50% = the time needed to attain 50% of a steady-state signal) compared to the 2D biosensor configuration with t50% = 354 s. The 3D glycan biosensor was finally applied for the analysis of a human serum sample spiked with an analyte.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

    Part of the 1994 Industrial Minerals Review. The production, consumption, and applications of construction aggregates are reviewed. In 1994, the production of construction aggregates, which includes crushed stone and construction sand and gravel combined, increased 7.7 percent to 2.14 Gt compared with the previous year. These record production levels are mostly a result of funding for highway construction work provided by the Intermodal Surface Transportation Efficiency Act of 1991. Demand is expected to increase for construction aggregates in 1995.

  2. Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.

    PubMed

    Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Havrila, Marek; Šponer, Jiří; Otyepka, Michal

    2017-03-23

    The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the α/γ = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical α/γ backbone conformations was analyzed with two AMBER force fields, ff99bsc0χOL3 and ff99bsc0χOL3 with the recent εζOL1 and βOL1 corrections for DNA. Although some α/γ substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer α/γ = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement.

  3. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    SciTech Connect

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-07

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  4. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

    PubMed

    Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

    2013-06-17

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.

  5. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    NASA Astrophysics Data System (ADS)

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-01

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  6. Oxidation Responsive Polymers with a Triggered Degradation via Arylboronate Self-Immolative Motifs on a Polyphosphazene Backbone

    PubMed Central

    2017-01-01

    Oxidation responsive polymers with triggered degradation pathways have been prepared via attachment of self-immolative moieties onto a hydrolytically unstable polyphosphazene backbone. After controlled main-chain growth, postpolymerization functionalization allows the preparation of hydrolytically stable poly(organo)phosphazenes decorated with a phenylboronic ester caging group. In oxidative environments, triggered cleavage of the caging group is followed by self-immolation, exposing the unstable glycine-substituted polyphosphazene which subsequently undergoes to backbone degradation to low-molecular weight molecules. As well as giving mechanistic insights, detailed GPC and 1H and 31P NMR analysis reveal the polymers to be stable in aqueous solutions, but show a selective, fast degradation upon exposure to hydrogen peroxide containing solutions. Since the post-polymerization functionalization route allows simple access to polymer backbones with a broad range of molecular weights, the approach of using the inorganic backbone as a platform significantly expands the toolbox of polymers capable of stimuli-responsive degradation. PMID:28251035

  7. Influence of backbone rigidness on single chain conformation of thiophene-based conjugated polymers.

    PubMed

    Hu, Zhongjian; Liu, Jianhua; Simón-Bower, Lauren; Zhai, Lei; Gesquiere, Andre J

    2013-04-25

    Structural order of conjugated polymers at different length scales directs the optoelectronic properties of the corresponding materials; thus it is of critical importance to understand and control conjugated polymer morphology for successful application of these materials in organic optoelectronics. Herein, with the aim of probing the dependence of single chain folding properties on the chemical structure and rigidness of the polymer backbones, single molecule fluorescence spectroscopy was applied to four thiophene-based conjugated polymers. These include regioregular poly(3-hexylthiophene) (RR-P3HT), poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-14), poly(2,5-bis(3-tetradecylthiophen-2-yl)thiophene-2-yl)thiophen-2-ylthiazolo[5,4-d]thiazole) (PTzQT-12), and poly(3,3-didodecylquaterthiophene)] (PQT-12). Our previous work has shown that RR-P3HT and PBTTT-14 polymer chains fold in their nanostructures, whereas PQT-12 and PTzQT-12 do not fold in their nanostructures. At the single molecule level, it was found that RR-P3HT single chains almost exclusively fold into loosely and strongly aggregated conformations, analogous to the folding properties in nanostructures. PQT-12 displays significant chain folding as well, but only into loosely aggregated conformations, showing an absence of strongly aggregated polymer chains. PBTTT-14 exhibits a significant fraction of rigid polymer chain. The findings made for single molecules of PQT-12 and PBTTT-14 are thus in contrast with the observations made in their corresponding nanostructures. PTzQT-12 appears to be the most rigid and planar conjugated polymer of these four polymers. However, although the presumably nonfolding polymers PQT-12 and PTzQT-12 exhibit less folding than RR-P3HT, there is still a significant occurrence of chain folding for these polymers at the single molecule level. These results suggest that the folding properties of conjugated polymers can be influenced by the architecture of the

  8. Dual-functional ROMP-based betaines: effect of hydrophilicity and backbone structure on nonfouling properties.

    PubMed

    Colak, Semra; Tew, Gregory N

    2012-01-10

    Foundational materials for nonfouling coatings were designed and synthesized from a series of novel dual-functional zwitterionic polymers, Poly[NRZI], which were easily obtained via ring-opening metathesis polymerization (ROMP) followed by a single step transformation of the cationic precursor, Poly[NR(+)], to the zwitterion, Poly[NRZI]. The resulting unique dual-functional structure contained the anion and the cation within the same repeat unit but on separate side chains, enabling the hydrophilicity of the system to be tuned at the repeat unit level. These dual-functional zwitterionic polymers were specifically designed to investigate the impact of structural changes, including the backbone, hydrophilicity, and charge, on the overall nonfouling properties. To evaluate the importance of backbone structure, and as a direct comparison to previously studied methacrylate-based betaines, norbornene-based carbo- and sulfobetaines (Poly[NCarboZI] and Poly[NSulfoZI]) as well as a methacrylate-based sulfobetaine (Poly[MASulfoZI]) were synthesized. These structures contain the anion-cation pairs on the same side chain. Nonfouling coatings were prepared from copolymers, composed of the zwitterionic/cationic precursor monomer and an ethoxysilane-containing monomer. The coatings were evaluated by using protein adsorption studies, which clearly indicated that the overall hydrophilicity has a major influence on the nonfouling character of the materials. The most hydrophilic coating, from the oligoethylene glycol (OEG)-containing dual-functional betaine, Poly[NOEGZI-co-NSi], showed the best resistance to nonspecific protein adsorption (Γ(FIB) = 0.039 ng/mm(2)). Both norbornene-based polymers systems, Poly[NSulfoZI] and Poly[NCarboZI], were more hydrophilic and thus more resistant to protein adsorption than the methacrylate-based Poly[MASulfoZI]. Comparing the protein resistance of the dual-functional zwitterionic coatings, Poly[NRZI-co-NSi], to that of their cationic

  9. Epitaxy-assisted creation of PCBM nanocrystals and its application in constructing optimized morphology for bulk-heterojunction polymer solar cells.

    PubMed

    Li, Ligui; Lu, Guanghao; Li, Sijun; Tang, Haowei; Yang, Xiaoniu

    2008-12-11

    PCBM (a C60 derivative) is so far the most successful electron acceptor for bulk-heterojunction polymer photovoltaic (PV) cells. Here we present a novel method epitaxy-assisted creation of PCBM nanocrystals and their homogeneous distribution in the matrix using freshly cleaved mica sheet as the substrate. The highly matched epitaxy relationship between the unit cell of PCBM crystal and crystallographic (001) surface of mica induces abundant PCBM nuclei, which subsequently develop into nanoscale crystals with homogeneous dispersion in the composite film. Both the shape and size of these nanocrystals could be tuned via choosing the type of matrix polymer, film thickness, ratio of PCBM in the composite film, and annealing temperature. Thus, the obtained thin composite film is removed from the original mica substrate via the flotation technique and transferred to a real substrate for device completion. The success of this method has been verified by the substantially improved device performance, in particular the increased short-circuit current, which is heavily dependent on the morphology of the photoactive layer. Therefore, we have actually demonstrated a novel approach to construct preferred morphology for high-performance optoelectronic devices via resorting to other specific substrates which could induce the formation of this type morphology.

  10. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    NASA Astrophysics Data System (ADS)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

    2016-06-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

  11. Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis.

    PubMed

    Gil, Victor A; Lecina, Daniel; Grebner, Christoph; Guallar, Victor

    2016-10-15

    Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application in exploring protein flexibility by using the Monte Carlo method PELE. This new method alternates two different stages, a perturbation of the backbone through the application of torsional normal modes, and a resampling of the side chains. We have evaluated the new approach using two test systems, ubiquitin and c-Src kinase, and the differences to the original ANM method are assessed by comparing both results to reference molecular dynamics simulations. The results suggest that the sampled phase space in the internal coordinate approach is closer to the molecular dynamics phase space than the one coming from a Cartesian coordinate anisotropic network model. In addition, the new method shows a great speedup (∼5-7×), making it a good candidate for future normal mode implementations in Monte Carlo methods.

  12. Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution.

    PubMed

    Fernández-López, Raúl; Garcillán-Barcia, M Pilar; Revilla, Carlos; Lázaro, Miguel; Vielva, Luis; de la Cruz, Fernando

    2006-11-01

    Plasmids cannot be understood as mere tools for genetic exchange: they are themselves subject to the forces of evolution. Their genomic and phylogenetic features have been less studied in this respect. Focusing on the IncW incompatibility group, which includes the smallest known conjugative plasmids, we attempt to unveil some common trends in plasmid evolution. The functional modules of IncW genetic backbone are described, with emphasis on their architecture and relationships to other plasmid groups. Some plasmid regions exhibit strong phylogenetic mosaicism, in striking contrast to others of unusual synteny conservation. The presence of genes of unknown function that are widely distributed in plasmid genomes is also emphasized, exposing the existence of ill-defined yet conserved plasmid functions. Conjugation is an essential hallmark of IncW plasmid biology and special attention is given to the organization and evolution of its transfer modules. Genetic exchange between plasmids and their hosts is analysed by following the evolution of the type IV secretion system. Adaptation of the trw conjugative machinery to pathogenicity functions in Bartonella is discussed as an example of how plasmids can change their host modus vivendi. Starting from the phage paradigm, our analysis articulates novel concepts that apply to plasmid evolution.

  13. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    PubMed Central

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  14. Is there a Climate Network - A Backbone of the Climate System? (Invited)

    NASA Astrophysics Data System (ADS)

    Kurths, J.

    2010-12-01

    We consider an inverse problem: Is there a backbone-like structure underlying the climate system? For this we propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system. This technique is then applied to reanalysis and model surface air temperature data. Parameters of this network, as betweenness centrality, uncover relations to global circulation patterns in oceans and atmosphere. We especially study the role of hubs and of long range connections, called teleconnections, in the flows of energy and matter in the climate system. The global scale view on climate networks offers promising new perspectives for detecting dynamical structures based on nonlinear physical processes in the climate system. References Arenas, A., A. Diaz-Guilera, J. Kurths, Y. Moreno, and C. Zhou, Phys. Reports 2008, 469, 93. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europ. Phys. J. ST 2009, 174, 157-179. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europhys. Lett. 2009, 87, 48007. Nawrath, J. et al., Phys. Rev. Lett. 2010, 104, 038701. Donner, R., Y. Zou, J. Donges, N. Marwan, and J. Kurths, Phys. Rev. E 2010, 81, 015101(R ).

  15. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    PubMed

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web.

  16. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    PubMed

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

  17. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

    PubMed Central

    Cino, Elio A.; Soares, Iaci N.; Pedrote, Murilo M.; de Oliveira, Guilherme A. P.; Silva, Jerson L.

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  18. Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review

    PubMed Central

    Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

    2014-01-01

    Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

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

    PubMed Central

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael; Pedrini, Bill; Herrmann, Torsten; Wüthrich, Kurt

    2014-01-01

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90% of the residues. For most proteins the APSY data acquisition was completed in less than 30 hours. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. PMID:25428764

  20. Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR

    PubMed Central

    Knight, Michael J.; Pell, Andrew J.; Bertini, Ivano; Felli, Isabella C.; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

    2012-01-01

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu+ (diamagnetic) or Cu2+ (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to 1H-1H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a Gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable. PMID:22723345

  1. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers.

    PubMed

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clément; Ratel, Olivier; Tassone, Christopher; Toney, Michael F; Beaujuge, Pierre M

    2014-11-26

    Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b']dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  2. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    PubMed Central

    Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

    2010-01-01

    An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability. PMID:22294890

  3. Ionization Cross Sections and Dissociation Channels of the DNA Sugar-Phosphate Backbone by Electron Collisions

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher; Huo, Winifred M.; Fletcher, Graham D.

    2004-01-01

    It has been suggested that the genotoxic effects of ionizing radiation in living cells are not caused by the highly energetic incident radiation, but rather are induced by less energetic secondary species generated, the most abundant of which are free electrons.' The secondary electrons will further react to cause DNA damage via indirect and direct mechanisms. Detailed knowledge of these mechanisms is ultimately important for the development of global models of cellular radiation damage. We are studying one possible mechanism for the formation cf DNA strand breaks involving dissociative ionization of the DNA sugar-phosphate backbone induced by secondary electron co!lisions. We will present ionization cross sections at electron collision energies between threshold and 10 KeV using the improved binary encounter dipole (iBED) formulation' Preliminary results of the possible dissociative ionization pathways will be presented. It is speculated that radical fragments produced from the dissociative ionization can further react, providing a possible mechanism for double strand breaks and base damage.

  4. An enhanced backbone-assisted reliable framework for wireless sensor networks.

    PubMed

    Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

    2010-01-01

    An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

  5. Effect of Bulky Substituents in the Polymer Backbone on the Properties of Polyimide Aerogels.

    PubMed

    Viggiano, Rocco P; Williams, Jarrod C; Schiraldi, David A; Meador, Mary Ann B

    2017-03-08

    With unique advantages over inorganic aerogels including higher strengths and compressive moduli, greater toughness, and the ability to be fabricated as a flexible thin film, polymer aerogels have the potential to supplant inorganic aerogels in numerous applications. Among polymer aerogels, polyimide aerogels possess a high degree of high thermal stability as well as outstanding mechanical properties. However, while the onset of thermal decomposition for these materials is typically very high (greater than 500 °C), the polyimide aerogels undergo dramatic thermally induced shrinkage at temperatures well below their glass transition (Tg) or decomposition temperature, which limits their use. In this study, we show that shrinkage is reduced when a bulky moiety is incorporated in the polymer backbone. Twenty different formulations of polyimide aerogels were synthesized from 3,3,'4,4'-biphenyltetracarboxylic dianhydride (BPDA) and 4,4'-oxidianiline (ODA) or a combination of ODA and 9,9'-bis(4-aminophenyl)fluorene (BAPF) and cross-linked with 1,3,5-benzenetricarbonyl trichloride (BTC) in a statistically designed study. The polymer concentration, n-value, and molar concentration of ODA and BAPF were varied to demonstrate the effect of these variables on certain properties. Samples containing BAPF showed a reduction in shrinkage by as much as 50% after aging at elevated temperatures for 500 h compared to those made with ODA alone.

  6. Mechanics and chemistry: single molecule bond rupture forces correlate with molecular backbone structure.

    PubMed

    Frei, Michael; Aradhya, Sriharsha V; Koentopp, Max; Hybertsen, Mark S; Venkataraman, L

    2011-04-13

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 ± 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

  7. Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry.

    PubMed

    Barondeau, David P; Kassmann, Carey J; Tainer, John A; Getzoff, Elizabeth D

    2005-02-15

    The Aequorea victoria green fluorescent protein (GFP) undergoes a remarkable post-translational modification to create a chromophore out of its component amino acids S65, Y66, and G67. Here, we describe mutational experiments in GFP designed to convert this chromophore into a 4-methylidene-imidazole-5-one (MIO) moiety similar to the post-translational active-site electrophile of histidine ammonia lyase (HAL). Crystallographic structures of GFP variant S65A Y66S (GFPhal) and of four additional related site-directed mutants reveal an aromatic MIO moiety and mechanistic details of GFP chromophore formation and MIO biosynthesis. Specifically, the GFP scaffold promotes backbone cyclization by (1) favoring nucleophilic attack by close proximity alignment of the G67 amide lone pair with the pi orbital of the residue 65 carbonyl and (2) removing enthalpic barriers by eliminating inhibitory main-chain hydrogen bonds in the precursor state. GFP R96 appears to induce structural rearrangements important in aligning the molecular orbitals for ring cyclization, favor G67 nitrogen deprotonation through electrostatic interactions with the Y66 carbonyl, and stabilize the reduced enolate intermediate. Our structures and analysis also highlight negative design features of the wild-type GFP architecture, which favor chromophore formation by destabilizing alternative conformations of the chromophore tripeptide. By providing a molecular basis for understanding and controlling the driving force and protein chemistry of chromophore creation, this research has implications for expansion of the genetic code through engineering of modified amino acids.

  8. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings.

    PubMed

    Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

    2015-02-04

    Three-bond (3)J(C'C') and (3)J(HNHα) couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, (3)J(HNHα) is tightly correlated with (3)J(C'C'), but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be extracted from (3)J(C'C') and (3)J(HNHα), as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of (3)J(C'C') and (3)J(HNH) couplings at very high precision, and impact of factors other than the intervening torsion angle on (3)J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of α-synuclein yields rather homogeneous widths of 69 ± 6° for the ϕ angle distributions and (3)J(C'C') values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and (1)H-(1)H NOEs. Data are consistent with a modest (≤30%) population of the polyproline II region.

  9. Essential roles of four-carbon backbone chemicals in the control of metabolism

    PubMed Central

    Chriett, Sabrina; Pirola, Luciano

    2015-01-01

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyrate-related molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance. PMID:26322177

  10. Essential roles of four-carbon backbone chemicals in the control of metabolism.

    PubMed

    Chriett, Sabrina; Pirola, Luciano

    2015-08-26

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyrate-related molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance.

  11. Design and Construction of a High Energy X-Ray R and D Facility, and the Development and Optimization of Real Time Radioisotopic Characterization of Remote Handled Waste at MeV Energies

    SciTech Connect

    Halliwell, S.; Georgiev, G.

    2007-07-01

    Real time radioscopy (RTR) is used extensively for the non-destructive examination (NDE) modality in the characterization of waste using x-ray energies of up to 450 keV. The majority of contact handled waste in drums and boxes such as the standard waste box (SWB) and the B25 box, can be penetrated by x-rays at these energies. However, the shielding within remote handled (RH) waste packages, the high density of many waste matrices, and the large size of other waste packages containing both remote handled and contact handled waste, require x-rays at MeV energies, in order to penetrate the waste matrices to enable x-ray images to be made. To develop, optimize and validate the performance of high energy x-ray imaging systems, requires a shielded vault complete with remote handling equipment for the manipulation of the x-ray generating equipment, the imaging chain, and the surrogate waste being inspected. This paper describes the design and construction of a High Energy X-Ray, R and D facility, and the results of the initial program of work to optimize systems for the real time inspection of RH waste. (authors)

  12. Electrochemical construction

    DOEpatents

    Einstein, Harry; Grimes, Patrick G.

    1983-08-23

    An electrochemical cell construction features a novel co-extruded plastic electrode in an interleaved construction with a novel integral separator-spacer. Also featured is a leak and impact resistant construction for preventing the spill of corrosive materials in the event of rupture.

  13. Combinations of various CpG motifs cloned into plasmid backbone modulate and enhance protective immunity of viral replicon DNA anthrax vaccines.

    PubMed

    Yu, Yun-Zhou; Ma, Yao; Xu, Wen-Hui; Wang, Shuang; Sun, Zhi-Wei

    2015-08-01

    DNA vaccines are generally weak stimulators of the immune system. Fortunately, their efficacy can be improved using a viral replicon vector or by the addition of immunostimulatory CpG motifs, although the design of these engineered DNA vectors requires optimization. Our results clearly suggest that multiple copies of three types of CpG motifs or combinations of various types of CpG motifs cloned into a viral replicon vector backbone with strong immunostimulatory activities on human PBMC are efficient adjuvants for these DNA vaccines to modulate and enhance protective immunity against anthrax, although modifications with these different CpG forms in vivo elicited inconsistent immune response profiles. Modification with more copies of CpG motifs elicited more potent adjuvant effects leading to the generation of enhanced immunity, which indicated a CpG motif dose-dependent enhancement of antigen-specific immune responses. Notably, the enhanced and/or synchronous adjuvant effects were observed in modification with combinations of two different types of CpG motifs, which provides not only a contribution to the knowledge base on the adjuvant activities of CpG motifs combinations but also implications for the rational design of optimal DNA vaccines with combinations of CpG motifs as "built-in" adjuvants. We describe an efficient strategy to design and optimize DNA vaccines by the addition of combined immunostimulatory CpG motifs in a viral replicon DNA plasmid to produce strong immune responses, which indicates that the CpG-modified viral replicon DNA plasmid may be desirable for use as vector of DNA vaccines.

  14. Sustainable construction: construction and demolition waste reconsidered.

    PubMed

    del Río Merino, Mercedes; Izquierdo Gracia, Pilar; Weis Azevedo, Isabel Salto

    2010-02-01

    Construction activity in Europe has increased substantially in the past decade. Likewise, there has also been a commensurate rise in the generation of construction and demolition waste (C&DW). This, together with the fact that in many European countries the rate of recycling and reuse of C&DW is still quite low has engendered a serious environmental problem and a motivation to develop strategies and management plans to solve it. Due to its composition, there is a significant potential to reuse and/or recycle C&DW, and thereby, contribute to improving the sustainability of construction and development, but practical procedures are not yet widely known or practiced in the construction industry. This article (a) summarizes the different applications that are presently practiced to optimize the recovery and/or application of C&DW for reuse, and (b) proposes various measures and strategies to improve the processing of this waste. The authors suggest that to enhance environmental effectiveness, a conscious and comprehensive C&DW management plan should be implemented in each jurisdiction. More precisely, this study presents a holistic approach towards C&DW management, through which environmental benefits can be achieved through the application of new construction methods that can contribute to sustainable growth.

  15. Interactions of TRIS [tris(hydroxymethyl)aminomethane] and related buffers with peptide backbone: thermodynamic characterization.

    PubMed

    Taha, Mohamed; Lee, Ming-Jer

    2010-10-21

    In a situation which is far from ideal, many buffers have been found to be quite reactive, besides maintaining their stable pH values. On the basis of apparent transfer free energies (ΔG(tr)'), through solubility measurements the interactions of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), and tetraglycine (Gly(4)), with several common neutral pH, amine-based buffers have been studied. The biological buffers studied in this work, including TRIS, TES, TAPS, TAPSO, and TABS are structurally related and all contain TRIS groups. These buffers have pK(a) values ranging from 7.5-9.0, which allow them to be used in biological, biochemical or environmental studies. We observed negative values of ΔG(tr)' for Gly(3) and Gly(4) from water to buffer, indicating that the interactions are favorable. However, the ΔG(tr)' values are positive for Gly and Gly(2), revealing unfavorable interactions, which except for the latter in TRIS buffer are negative. The surprising result in our data is the unexpected extraordinarily high favorable interactions between TRIS buffer and peptides (in comparison with the effect of the most common denaturants, urea and guanidine hydrochloride). The transfer free energies (ΔG(tr)') of the peptide backbone unit (-CH(2)C=O-NH-) contributions have been estimated from ΔG(tr)' values. We have also investigated the interactions of TRIS buffer with Bovine Serum Albumin (BSA), as a globular protein, using dynamic light scattering (DLS), zeta potential, UV-Visible absorption, fluorescence and Raman spectroscopy measurements. The results indicated that TRIS buffer stabilized the BSA molecules.

  16. Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules.

    PubMed

    Recktenwald, Jürgen; Shawky, Riham; Puk, Oliver; Pfennig, Frank; Keller, Ulrich; Wohlleben, Wolfgang; Pelzer, Stefan

    2002-04-01

    During analysis of the recently identified gene cluster for the glycopeptide antibiotic balhimycin, produced by Amycolatopsis mediterranei DSM 5908, novel genes were identified and characterized in detail. The gene products of four of the identified genes (bpsA, bpsB, bpsC and bpsD) are nonribosomal peptide synthetases (NRPSs); one (Orf1-protein) shows similarities to small proteins associated with several NRPSs without an assigned function. BpsA and BpsB are composed of three modules each (modules 1-6), BpsC of one module (module 7) and BpsD of a minimal module (module 8). Thus, the balhimycin gene cluster encodes eight modules, whereas its biosynthetic product is a heptapeptide. Non-producing mutants were created by a gene disruption of bpsB, an in-frame deletion of bpsC and a gene replacement of bpsD. After establishment of a gene complementation system for Amycolatopsis strains, the replacement mutant of bpsD was complemented, demonstrating for the first time that BpsD, encoding the eighth module, is indeed involved in balhimycin biosynthesis. After feeding with beta-hydroxytyrosine the capability of the bpsD mutant to produce balhimycin was restored, demonstrating the participation of BpsD in the biosynthesis of this amino acid. The specificity of four of the eight adenylation domains was determined by ATP/PP(i) exchange assays: modules 4 and 5 activated L-4-hydroxyphenylglycine, module 6 activated beta-hydroxytyrosine and module 7 activated L-3,5-dihydroxyphenylglycine, which is in accordance with the sequence of the non-proteogenic amino acids 4 to 7 of the balhimycin backbone.

  17. Backbones in the parameter plane of the Hénon map

    NASA Astrophysics Data System (ADS)

    Falcolini, Corrado; Tedeschini-Lalli, Laura

    2016-01-01

    Parameter plane (b, a) of the real Hénon map has been investigated for curves of bifurcation, curves of homoclinic heteroclinic onsets, and also searching for borders of areas variously characterized. Such curves are, in general, complicated and show singularities. Pieces of two monotone curves, spanning the (b, a) parameter plane of the real Hénon map, can be detected in four quite different studies appeared along the years 1982-2008. We study the extent of their similarity to read and interpret them into the same curves. To us, these two curves are the accumulation loci of bifurcation curves of two principal families of periodic sinks of type "period-adding machine." We call them "backbones," because they are monotone; moreover, they are the borders of some important regions in the (b, a)-plane. Hamouly and Mira in 1982 [C. R. Acad. Sc. Paris1 293, 525-528 (1982)] studied the structure of bifurcation of periodic orbits and their mutual position and intersection. Gonchenko et al. [SIAM J. Appl. Dyn. Syst. 4, 407-436 (2005)] display the continuation (in parameter plane) of the first heteroclinic connection and of the first homoclinic connection between the two fixed points of the map. Alligood and Sauer [Commun. Math. Phys. 120, 105-119 (1988)] studied parameter regions characterized by the same rotation number of the "accessible" periodic saddle. Finally, Lorenz [Physica D 237, 1689-1704 (2008)] in 2008 draws areas in the parameter plane statistically characterized by a finite attractor. In this paper, we show how these criteria interact. We therefore conjecture that the wealth of curves of homoclinic onsets could be in general hierarchized by the structure of accessible saddles.

  18. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone.

    PubMed

    Sampedro, Javier; Valdivia, Elene R; Fraga, Patricia; Iglesias, Natalia; Revilla, Gloria; Zarra, Ignacio

    2017-02-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3 In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1 We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer.

  19. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases.

    PubMed

    Nyffenegger, Christian; Nordvang, Rune Thorbjørn; Zeuner, Birgitte; Łężyk, Mateusz; Difilippo, Elisabetta; Logtenberg, Madelon J; Schols, Henk A; Meyer, Anne S; Mikkelsen, Jørn Dalgaard

    2015-10-01

    This paper describes the discovery and characterization of two novel β-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as β-N-acetylglucosamine (GlcNAc) donor. The enzyme-encoding genes were identified by functional screening of a soil-derived metagenomic library. The β-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest homologues are 59 % for HEX1 and 51 % for HEX2 on the protein level. Both β-N-acetylhexosaminidases are classified into glycosyl hydrolase family 20 (GH 20) are able to hydrolyze para-nitrophenyl-β-N-acetylglucosamine (pNP-GlcNAc) as well as para-nitrophenyl-β-N-acetylgalactosamine (pNP-GalNAc) and exhibit pH optima of 8 and 6 for HEX1 and HEX2, respectively. The enzymes are able to hydrolyze N-acetylchitooligosaccharides with a degree of polymerization of two, three, and four. The major findings were, that HEX1 and HEX2 catalyze trans-glycosylation reactions with lactose as acceptor, giving rise to the human milk oligosaccharide precursor lacto-N-triose II (LNT2) with yields of 2 and 8 % based on the donor substrate. In total, trans-glycosylation reactions were tested with the disaccharide acceptors β-lactose, sucrose, and maltose, as well as with the monosaccharides galactose and glucose resulting in the successful attachment of GlcNAc to the acceptor in all cases.

  20. Identification of high-affinity P2Y₁₂ antagonists based on a phenylpyrazole glutamic acid piperazine backbone.

    PubMed

    Zech, Gernot; Hessler, Gerhard; Evers, Andreas; Weiss, Tilo; Florian, Peter; Just, Melitta; Czech, Jörg; Czechtizky, Werngard; Görlitzer, Jochen; Ruf, Sven; Kohlmann, Markus; Nazaré, Marc

    2012-10-25

    A series of novel, highly potent P2Y₁₂ antagonists as inhibitors of platelet aggregation based on a phenylpyrazole glutamic acid piperazine backbone is described. Exploration of the structural requirements of the substituents by probing the structure-activity relationship along this backbone led to the discovery of the N-acetyl-(S)-proline cyclobutyl amide moiety as a highly privileged motif. Combining the most favorable substituents led to remarkably potent P2Y₁₂ antagonists displaying not only low nanomolar binding affinity to the P2Y₁₂ receptor but also a low nanomolar inhibition of platelet aggregation in the human platelet rich plasma assay with IC₅₀ values below 50 nM. Using a homology and a three-dimensional quantitative structure-activity relationship model, a binding hypothesis elucidating the impact of several structural features was developed.

  1. Progress in palladium-based catalytic systems for the sustainable synthesis of annulated heterocycles: a focus on indole backbones.

    PubMed

    Platon, Mélanie; Amardeil, Régine; Djakovitch, Laurent; Hierso, Jean-Cyrille

    2012-05-21

    A survey highlighting the most recent palladium catalytic systems produced and their performances for progress in direct synthesis of indole backbones by heterocarbocyclization of reactive substrates is provided. The discussion is developed in relation with the principles of sustainable chemistry concerning atom and mass economy. In this respect, the general convergent character of the syntheses is of particular interest (one-pot, domino, cascade or tandem reactions), and the substrates accessibility and reactivity, together with the final waste production, are also important. This critical review clearly indicates that the development of ligand chemistry, mainly phosphines and carbenes, in the last few decades gave a significant impetus to powerful functionalization of indoles at virtually all positions of this ubiquitous backbone (118 references).

  2. Role of monomer sequence and backbone structure in polypeptoid and polypeptide polymers for anti-fouling applications

    NASA Astrophysics Data System (ADS)

    Patterson, Anastasia; Rizis, Georgios; Wenning, Brandon; Finlay, John; Ober, Christopher; Segalman, Rachel

    Polymeric coatings rely on a fine balance of surface properties to achieve biofouling resistance. Bioinsipired polymers and oligomers provide a modular strategy for the inclusion of multiple functionalities with controlled architecture, sequence and surface properties. In this work, polypeptoid and polypeptide functionalized coatings based on PEO and PDMS block copolymers were compared with respect to surface presentation and fouling by Ulva linza. While polypeptoids and polypeptides are simple isomers of each other, the lack of backbone chirality and hydrogen bonding in polypeptoids leads to surprisingly different surface behavior. Specifically, the polypeptoids surface segregate much more strongly than analogous polypeptide functionalized polymers, which in turn affects the performance of the coating. Indeed, polypeptoid functionalized surfaces were significantly better both in terms of anti-fouling and fouling release than the corresponding polypeptide-bearing polymers. The role of specific monomer sequence and backbone chemistry will be further discussed in this poster.

  3. Free vibration analysis of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses

    NASA Astrophysics Data System (ADS)

    Coral, W.; Rossi, C.; Curet, O. M.

    2015-12-01

    This paper presents a Differential Quadrature Element Method for free transverse vibration of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses (fish ribs). The proposed method is based on the theory of a Timoshenko cantilever beam. The effects of the masses (number, magnitude and position) on the value of natural frequencies are investigated. Governing equations, compatibility and boundary conditions are formulated according to the Differential Quadrature rules. The convergence, efficiency and accuracy are compared to other analytical solution proposed in the literature. Moreover, the proposed method has been validate against the physical prototype of a flexible fish backbone. The main advantages of this method, compared to the exact solutions available in the literature are twofold: first, smaller computational cost and second, it allows analysing the free vibration in beams whose section is an arbitrary function, which is normally difficult or even impossible with other analytical methods.

  4. Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone.

    PubMed

    Stevens, Kristof; Claeys, Diederica D; Catak, Saron; Figaroli, Sara; Hocek, Michal; Tromp, Jan M; Schürch, Stefan; Van Speybroeck, Veronique; Madder, Annemieke

    2011-06-14

    Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.

  5. A novel dengue virus serotype 1 vaccine candidate based on Japanese encephalitis virus vaccine strain SA14-14-2 as the backbone.

    PubMed

    Yang, Huiqiang; Li, Zhushi; Lin, Hua; Wang, Wei; Yang, Jian; Liu, Lina; Zeng, Xianwu; Wu, Yonglin; Yu, Yongxin; Li, Yuhua

    2016-06-01

    To develop a potential dengue vaccine candidate, a full-length cDNA clone of a novel chimeric virus was constructed using recombinant DNA technology, with Japanese encephalitis virus (JEV) vaccine strain SA14-14-2 as the backbone, with its premembrane (prM) and envelope (E) genes substituted by their counterparts from dengue virus type 1 (DENV1). The chimeric virus (JEV/DENV1) was successfully recovered from primary hamster kidney (PHK) cells by transfection with the in vitro transcription products of JEV/DENV1 cDNA and was identified by complete genome sequencing and immunofluorescent staining. No neuroinvasiveness of this chimeric virus was observed in mice inoculated by the subcutaneous route (s.c.) or by the intraperitoneal route (i.p.), while some neurovirulence was displayed in mice that were inoculated directly by the intracerebral route (i.c.). The chimeric virus was able to stimulate high-titer production of antibodies against DENV1 and provided protection against lethal challenge with neuroadapted dengue virus in mice. These results suggest that the chimeric virus is a promising dengue vaccine candidate.

  6. Large and ultrafast third-order optical nonlinearity of novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in backbones

    NASA Astrophysics Data System (ADS)

    Huang, Wentao; Wang, Shufeng; Yang, Hong; Gong, Qihuang; Zhan, Xiaowei; Liu, Yunqi; Zhu, Daoben

    2001-12-01

    A femtosecond time-resolved optical Kerr gate method, using 115 fs laser pulses at 830 nm, has been applied to investigate the third-order nonlinearity of two novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in their backbones. Ultrafast off-resonant optical Kerr responses have been observed and the magnitude of the second-order hyperpolarizability was measured as large as 10 -30 esu. The origin of the extraordinary large value was explored and compared to other organic materials.

  7. Photoinduced bending behavior of cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone.

    PubMed

    Lv, Jiu-an; Wang, Weiru; Xu, Jixiang; Ikeda, Tomiki; Yu, Yanlei

    2014-07-01

    Cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone are synthesized by photoinitiated cationic copolymerization. Azobenzene moieties in the film surface toward the light source are simultaneously photoaligned during photopolymerization with unpolarized 436 nm light and thus form a splayed alignment in the whole film. The prepared films show reversible photoinduced bending behavior with opposite bending directions when different surfaces of one film face to ultraviolet light irradiation.

  8. Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space.

    PubMed

    Dahl, David B; Bohannan, Zach; Mo, Qianxing; Vannucci, Marina; Tsai, Jerry

    2008-05-02

    Grouping the 20 residues is a classic strategy to discover ordered patterns and insights about the fundamental nature of proteins, their structure, and how they fold. Usually, this categorization is based on the biophysical and/or structural properties of a residue's side-chain group. We extend this approach to understand the effects of side chains on backbone conformation and to perform a knowledge-based classification of amino acids by comparing their backbone phi, psi distributions in different types of secondary structure. At this finer, more specific resolution, torsion angle data are often sparse and discontinuous (especially for nonhelical classes) even though a comprehensive set of protein structures is used. To ensure the precision of Ramachandran plot comparisons, we applied a rigorous Bayesian density estimation method that produces continuous estimates of the backbone phi, psi distributions. Based on this statistical modeling, a robust hierarchical clustering was performed using a divergence score to measure the similarity between plots. There were seven general groups based on the clusters from the complete Ramachandran data: nonpolar/beta-branched (Ile and Val), AsX (Asn and Asp), long (Met, Gln, Arg, Glu, Lys, and Leu), aromatic (Phe, Tyr, His, and Cys), small (Ala and Ser), bulky (Thr and Trp), and, lastly, the singletons of Gly and Pro. At the level of secondary structure (helix, sheet, turn, and coil), these groups remain somewhat consistent, although there are a few significant variations. Besides the expected uniqueness of the Gly and Pro distributions, the nonpolar/beta-branched and AsX clusters were very consistent across all types of secondary structure. Effectively, this consistency across the secondary structure classes implies that side-chain steric effects strongly influence a residue's backbone torsion angle conformation. These results help to explain the plasticity of amino acid substitutions on protein structure and should help in

  9. P-Stereogenic bisphosphines with a hydrazine backbone: from N-N atropoisomerism to double nitrogen inversion.

    PubMed

    Prades, Amparo; Núñez-Pertíñez, Samuel; Riera, Antoni; Verdaguer, Xavier

    2017-04-10

    The synthesis of P-stereogenic bisphosphine ligands starting from a phosphinous acid chiral synthon and hydrazine is reported. The dialkylation of the hydrazine backbone yielded atropo- and nitrogen inversion isomers which are in slow exchange. The crystallization of one of the isomers allowed us to study the reaction kinetics of the equilibria. The new ligands were tested in the Rh catalysed asymmetric hydrogenation of various benchmark substrates attaining up to 99% ee.

  10. The effect of junction modes between backbones and side chains of polyimides on the stability of liquid crystal vertical alignment.

    PubMed

    Che, Xinyuan; Gong, Shiming; Zhang, Heng; Liu, Bin; Wang, Yinghan

    2016-02-07

    Polyimides (PI-N9 and PI-N12) were synthesized from two kinds of functional diamines, whose junction modes between backbones and side chains were different. Side chains of PI-N9 were linked to the backbones with an ether bond spacer; and side chains of PI-N12 were directly linked to the backbones without any spacer. The PI alignment layer surfaces were investigated by atomic force microscopy, surface free energy measurements, X-ray photo-electron spectroscopy and polarized attenuated total reflection Fourier transformed infrared spectroscopy. It was found that PI-N9 lost the vertical alignment capability after high-strength rubbing, while PI-N12 could still induce liquid crystals (LCs) to align vertically under the same condition. The mechanism of the macroscopic molecular orientation of the PI surface is proposed. During the high-strength rubbing process, the side chain could rotate around the flexible ether bond which existed between the side chain and the main chain of PI-N9 and then fell over. Therefore, PI-N9 could not induce the vertical alignment of LCs anymore. But PI-N12 could keep LCs aligning vertically all the time, which proved that the stability of LC alignment induced by PI-N12 was better.

  11. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    PubMed

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations.

  12. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    PubMed

    Ollikainen, Noah; de Jong, René M; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  13. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

    PubMed Central

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  14. 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme

    PubMed Central

    Kiryutin, Alexey S.; Kasymov, Rustem D.; Petrova, Darya V.; Endutkin, Anton V.; Popov, Alexander V.; Yurkovskaya, Alexandra V.; Fedechkin, Stanislav O.; Brockerman, Jacob A.; Zharkov, Dmitry O.; Smirnov, Serge L.

    2016-01-01

    8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of EcoRI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew—Dickerson dodecamer sequence notably reduced the EcoRI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar—phosphate backbone conformation, inducing a BI→BII transition. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the sequence-specific contacts formed by the enzyme with DNA, shifts the distribution of BI/BII backbone conformers. Based on our data, we propose that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein—DNA interface. PMID:27749894

  15. Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Dateo, Christopher E.

    2005-01-01

    The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

  16. Oxygen K edge scattering from bulk comb diblock copolymer reveals extended, ordered backbones above lamellar order-disorder transition

    DOE PAGES

    Kortright, Jeffrey Barrett; Sun, Jing; Spencer, Ryan K.; ...

    2016-12-14

    The evolution of molecular morphology in bulk samples of comb diblock copolymer pNdc12-b-pNte21 across the lamellar order-disorder transition (ODT) is studied using resonant x-ray scattering at the oxygen K edge, with the goal of determining whether the molecules remain extended or collapse above the ODT. The distinct spectral resonances of carbonyl oxygen on the backbone and ether oxygen in the pNte side chains combine with their different site symmetry within the molecule to yield strong differences in bulk structural sensitivity at all temperatures. Comparison with simple models for the disordered phase clearly reveals that disordering at the ODT corresponds tomore » loss of positional order of molecules with extended backbones that retain orientational order, rather than backbone collapse into a locally isotropic disordered phase. This conclusion is facilitated directly by the distinct structural sensitivity at the two resonances. Lastly, we discuss the roles of depolarized scattering in enhancing this sensitivity, and background fluorescence in limiting dynamic range, in oxygen resonant scattering.« less

  17. Oxygen K edge scattering from bulk comb diblock copolymer reveals extended, ordered backbones above lamellar order-disorder transition

    SciTech Connect

    Kortright, Jeffrey Barrett; Sun, Jing; Spencer, Ryan K.; Jiang, Xi; Zuckermann, Ronald N.

    2016-12-14

    The evolution of molecular morphology in bulk samples of comb diblock copolymer pNdc12-b-pNte21 across the lamellar order-disorder transition (ODT) is studied using resonant x-ray scattering at the oxygen K edge, with the goal of determining whether the molecules remain extended or collapse above the ODT. The distinct spectral resonances of carbonyl oxygen on the backbone and ether oxygen in the pNte side chains combine with their different site symmetry within the molecule to yield strong differences in bulk structural sensitivity at all temperatures. Comparison with simple models for the disordered phase clearly reveals that disordering at the ODT corresponds to loss of positional order of molecules with extended backbones that retain orientational order, rather than backbone collapse into a locally isotropic disordered phase. This conclusion is facilitated directly by the distinct structural sensitivity at the two resonances. Lastly, we discuss the roles of depolarized scattering in enhancing this sensitivity, and background fluorescence in limiting dynamic range, in oxygen resonant scattering.

  18. Comparative experimental investigation on the actuation mechanisms of ionic polymer–metal composites with different backbones and water contents

    SciTech Connect

    Zhu, Zicai; Chang, Longfei; Wang, Yanjie; Chen, Hualing; Asaka, Kinji; Zhao, Hongxia; Li, Dichen

    2014-03-28

    Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14 wt. %, Nafion–IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion–IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13 wt. %. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group –COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

  19. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

    PubMed Central

    Liu, Yingliang; Guchhait, Biswajit; Siebert, Torsten; Fingerhut, Benjamin P.; Elsaesser, Thomas

    2017-01-01

    Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

  20. Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Jayaraman, Arthi

    DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

    Part of the Annual Commodities Review 1995. Production of construction aggregates such as crushed stone and construction sand and gravel showed a marginal increase in 1995. Most of the 1995 increases were due to funding for highway construction work. The major areas of concern to the industry included issues relating to wetlands classification and the classification of crystalline silica as a probable human carcinogen. Despite this, an increase in demand is anticipated for 1996.

  2. 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

  3. Constructive Fun.

    ERIC Educational Resources Information Center

    Simanek, Donald E.

    1994-01-01

    Compares and reviews currently available brands of steel construction sets that are useful to physics teachers for building demonstrations, prototypes of mechanisms, robotics, and remote control devices. (ZWH)

  4. Optimally Stopped Optimization

    NASA Astrophysics Data System (ADS)

    Vinci, Walter; Lidar, Daniel A.

    2016-11-01

    We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark simulated annealing on a class of maximum-2-satisfiability (MAX2SAT) problems. We also compare the performance of a D-Wave 2X quantum annealer to the Hamze-Freitas-Selby (HFS) solver, a specialized classical heuristic algorithm designed for low-tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N =1098 variables, the D-Wave device is 2 orders of magnitude faster than the HFS solver, and, modulo known caveats related to suboptimal annealing times, exhibits identical scaling with problem size.

  5. Sequential Construction of Costly Networks

    SciTech Connect

    Gutfraind, Alexander

    2011-01-01

    Natural disasters or attacks often disrupt infrastructure networks requiring a costly recovery. This motivates an optimization problem where the objecitve is to construct the nodes of a graph G(V;E), and the cost of each node is dependent on the number of its neighbors previously constructed, or more generally, any properties of the previously-completed subgraph. In this optimization problem the objective is to find a permutation of the nodes which results in the least construction cost. We prove that in the case where the cost of nodes is a convex function in the number of neighbors, the optimal construction sequence is to start at a single node and move outwards. We also introduce algorithms and heuristics for solving various instances of the problem. Those methods can be applied to help reduce the cost of recovering from disasters as well as to plan the deployment of new network infrastructure.

  6. Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant.

    PubMed

    Song, Jikui; Markley, John L

    2003-05-13

    Standard mechanism protein inhibitors of serine proteinases bind as substrates and are cleaved by cognate proteinases at their reactive sites. The hydrolysis constant for this cleavage reaction at the P(1)-P(1)' peptide bond (K(hyd)) is determined by the relative concentrations at equilibrium of the "intact" (uncleaved, I) and "modified" (reactive site cleaved, I*) forms of the inhibitor. The pH dependence of K(hyd) can be explained in terms of a pH-independent term, K(hyd) degrees, plus the proton dissociation constants of the newly formed amino and carboxylate groups at the cleavage site. Two protein inhibitors that differ from one another by a single residue substitution have been found to have K(hyd) degrees values that differ by a factor of 5 [Ardelt, W., and Laskowski, M., Jr. (1991) J. Mol. Biol. 220, 1041-1052]: turkey ovomucoid third domain (OMTKY3) has K(hyd) degrees = 1.0, and Indian peafowl ovomucoid third domain (OMIPF3), which differs from OMTKY3 by the substitution P(2)'-Tyr(20)His, has K(hyd) degrees = 5.15. What mechanism is responsible for this small difference? Is it structural (enthalpic) or dynamic (entropic)? Does the mutation affect the free energy of the I state, the I* state, or both? We have addressed these questions through NMR investigations of the I and I forms of OMTKY3 and OMIPF3. Information about structure was derived from measurements of NMR chemical shift changes and trans-hydrogen-bond J-couplings; information about dynamics was obtained through measurements of (15)N relaxation rates and (1)H-(15)N heteronuclear NOEs with model-free analysis of the results. Although the I forms of each variant are more dynamic than the corresponding I forms, the study revealed no appreciable difference in the backbone dynamics of either intact inhibitor (OMIPF3 vs OMTKY3) or modified inhibitor (OMIPF3* vs OMTKY3*). Instead, changes in chemical shifts and trans-hydrogen-bond J-couplings suggested that the K(hyd) degrees difference arises from

  7. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.

    PubMed

    Deepak, R N V Krishna; Sankararamakrishnan, Ramasubbu

    2016-05-10

    Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.

  8. Design & construction.

    PubMed

    Souhrada, L

    1991-02-20

    The deepening recession hasn't slowed hospital construction activity--at least not yet. While experts say health care executives should expect fewer large projects within the next two years, as the result of unpredictable sources of capital and increasing censure of hospital capital spending, for the moment hospital projects are helping to shelter some design and construction firms from the recession's fallout.

  9. Design and Enantioselective Construction of Axially Chiral Naphthyl-Indole Skeletons.

    PubMed

    Zhang, Hong-Hao; Wang, Cong-Shuai; Li, Can; Mei, Guang-Jian; Li, Yuxue; Shi, Feng

    2017-01-02

    The first enantioselective construction of a new class of axially chiral naphthyl-indole skeletons has been established by organocatalytic asymmetric coupling reactions of 2-naphthols with 2-indolylmethanols (up to 99 % yield, 97:3 e.r.). This approach not only affords a new type of axially chiral heterobiaryl backbone, but also provides a new catalytic enantioselective strategy for constructing axially chiral biaryl scaffolds by making use of the C3-electrophilicity of 2-indolylmethanols.

  10. Constructing Phylogenies.

    ERIC Educational Resources Information Center

    Bilardello, Nicholas; Valdes, Linda

    1998-01-01

    Introduces a method for constructing phylogenies using molecular traits and elementary graph theory. Discusses analyzing molecular data and using weighted graphs, minimum-weight spanning trees, and rooted cube phylogenies to display the data. (DDR)

  11. Construction Administration.

    ERIC Educational Resources Information Center

    Barley, John McKim, II

    1986-01-01

    Successful completion of a construction project requires the efforts of a team composed of the owner, architect, and contractor. A preconstruction conference can clarify the roles of the team as specified in the design contract. (MLF)

  12. Construction aggregates

    USGS Publications Warehouse

    Nelson, T.I.; Bolen, W.P.

    2007-01-01

    Construction aggregates, primarily stone, sand and gravel, are recovered from widespread naturally occurring mineral deposits and processed for use primarily in the construction industry. They are mined, crushed, sorted by size and sold loose or combined with portland cement or asphaltic cement to make concrete products to build roads, houses, buildings, and other structures. Much smaller quantities are used in agriculture, cement manufacture, chemical and metallurgical processes, glass production and many other products.

  13. Differential backbone dynamics of companion helices in the extended helical coiled-coil domain of a bacterial chemoreceptor

    PubMed Central

    Bartelli, Nicholas L; Hazelbauer, Gerald L

    2015-01-01

    Cytoplasmic domains of transmembrane bacterial chemoreceptors are largely extended four-helix coiled coils. Previous observations suggested the domain was structurally dynamic. We probed directly backbone dynamics of this domain of the transmembrane chemoreceptor Tar from Escherichia coli using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. Spin labels were positioned on solvent-exposed helical faces because EPR spectra for such positions reflect primarily polypeptide backbone movements. We acquired spectra for spin-labeled, intact receptor homodimers solubilized in detergent or inserted into native E. coli lipid bilayers in Nanodiscs, characterizing 16 positions distributed throughout the cytoplasmic domain and on both helices of its helical hairpins, one amino terminal to the membrane-distal tight turn (N-helix), and the other carboxyl terminal (C-helix). Detergent solubilization increased backbone dynamics for much of the domain, suggesting that loss of receptor activities upon solubilization reflects wide-spread destabilization. For receptors in either condition, we observed an unanticipated difference between the N- and C-helices. For bilayer-inserted receptors, EPR spectra from sites in the membrane-distal protein-interaction region and throughout the C-helix were typical of well-structured helices. In contrast, for approximately two-thirds of the N-helix, from its origin as the AS-2 helix of the membrane-proximal HAMP domain to the beginning of the membrane-distal protein-interaction region, spectra had a significantly mobile component, estimated by spectral deconvolution to average approximately 15%. Differential helical dynamics suggests a four-helix bundle organization with a pair of core scaffold helices and two more dynamic partner helices. This newly observed feature of chemoreceptor structure could be involved in receptor function. PMID:26257396

  14. A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility.

    PubMed

    Berglund, Jennie; Angles d'Ortoli, Thibault; Vilaplana, Francisco; Widmalm, Göran; Bergenstråhle-Wohlert, Malin; Lawoko, Martin; Henriksson, Gunnar; Lindström, Mikael; Wohlert, Jakob

    2016-10-01

    The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ - ψ space and hydrogen-bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.

  15. An Unusual Conformational Isomer of Verrucosidin Backbone from a Hydrothermal Vent Fungus, Penicillium sp. Y-50-10

    PubMed Central

    Pan, Chengqian; Shi, Yutong; Auckloo, Bibi Nazia; Chen, Xuegang; Chen, Chen-Tung Arthur; Tao, Xinyi; Wu, Bin

    2016-01-01

    A new verrucosidin derivative, methyl isoverrucosidinol (1), was isolated from the marine fungus Penicillium sp. Y-50-10, dwelling in sulfur rich sediment in the Kueishantao hydrothermal vents off Taiwan. The structure was established by spectroscopic means including HRMS and 2D-NMR spectroscopic analysis. The absolute configuration was defined mainly by comparison of quantum chemical TDDFT calculated and experimental ECD spectra. Among hitherto known compounds with a verrucosidine backbone isolated from natural resource, compound 1 represents the first example of a new conformational isomer of its skeleton, exhibiting antibiotic activity against Bacillus subtilis with MIC value 32 μg/mL. PMID:27548192

  16. 1H, 15N and 13C backbone resonance assignments of the archetypal serpin α1-antitrypsin.

    PubMed

    Nyon, Mun Peak; Kirkpatrick, John; Cabrita, Lisa D; Christodoulou, John; Gooptu, Bibek

    2012-10-01

    Alpha(1)-antitrypsin is a 45-kDa (394-residue) serine protease inhibitor synthesized by hepatocytes, which is released into the circulatory system and protects the lung from the actions of neutrophil elastase via a conformational transition within a dynamic inhibitory mechanism. Relatively common point mutations subvert this transition, causing polymerisation of α(1)-antitrypsin and deficiency of the circulating protein, predisposing carriers to severe lung and liver disease. We have assigned the backbone resonances of α(1)-antitrypsin using multidimensional heteronuclear NMR spectroscopy. These assignments provide the starting point for a detailed solution state characterization of the structural properties of this highly dynamic protein via NMR methods.

  17. BON-BONs: cyclic molecules with a boron-oxygen-nitrogen backbone. Computational studies of their thermodynamic properties.

    PubMed

    Lawong, Aloysus K; Ball, David W

    2012-04-01

    Although they were first reported in 1963, molecules with a boron-oxygen-nitrogen dimeric backbone do not seem to have been investigated seriously in terms of thermodynamic properties. Here we report on the calculated structures and properties, including thermodynamics, of several so-called "BON-BON" molecules. With the popularity of nitrogen-containing substituents on new high-energy materials, nitro-substituted BON-BONs were a focus of our investigation. A total of 42 BON-BON molecules were evaluated, and thermochemical analysis shows a decrease in the specific enthalpy of combustion or decomposition with increasing NO(2) content, consistent with other systems.

  18. Design and Construction of Optimized Electrochemical Cell and Data Analysis System for Etching of Ion Tracks and Electro Deposition of Nano and Micro Wires in Porous Ion Tracks Foils

    NASA Astrophysics Data System (ADS)

    ShakeriJooybari, B.; Moghimi, R.; Golgiri, D.; Afarideh, H.; Lamehi-Rachti, M.; Ghergherehchi, M.

    In this work, an optimized computer controlled electrochemical cell were designed and constructed. This Electrolytic cell was used for etching latent ion tracks and electrochemical deposition of wires in pores of etched-ion tracks foils. The applied voltage and current through the electrochemical cell during the etching and electrodeposition were measured and monitored in real time by a Data Analysis system. Monitoring the current time curve during the filling of pores and growth of micro and nano wires allows one to stop the deposition process after a given time to obtain nano- and micro wire of a predefined length. In this work, Design and manufacture of a sealed electrochemical cell was done in a manner that one can change distance between electrodes and geometry of cathodes. Data analysis system was used to measuring and monitoring of applied voltage and current through the cell consists of three parts: Amplifier, Data acquisition (DAQ) system and Software. A current amplifier that used in data analysis system is a log ratio amplifier. A log ratio amplifier provides an output voltage proportional to the log base 10 of the ratio input current I1 (current during the electrodeposition of wire in cell) and Input current I2(flexible current of precision current source). A DAQ reading output voltage of amplifier and send to Computer. With lab view software analyzed the voltage and converted to the current corresponding to the electrodeposition of wires. Current amplifier designed and built in this work is a noise suppression that can measure small current through the cell with high accuracy. Advantage of proposed log ratio amplifier is one can used this amplifier for measuring and monitoring of current during the filling of pores and growth of wires in the etched ion track foils with various track density.

  19. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    NASA Astrophysics Data System (ADS)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  20. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: 2H NMR studies on perdeuterated C-phycocyanin.

    PubMed

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  1. Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

    PubMed

    Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

    2017-02-26

    Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs.

  2. Pemetrexed With Platinum Combination as a Backbone for Targeted Therapy in Non-Small-Cell Lung Cancer.

    PubMed

    Stinchcombe, Thomas E; Borghaei, Hossein; Barker, Scott S; Treat, Joseph Anthony; Obasaju, Coleman

    2016-01-01

    Standard platinum-based chemotherapy combinations for advanced non-small-cell lung cancer (NSCLC) have reached a plateau in terms of the survival benefit they offer for patients. In addition, the emerging clinical trend of tailored treatment based on patient characteristics has led to the development of therapeutic strategies that target specific cancer-related molecular pathways, including epidermal growth factor receptor (EGFR), angiogenesis, and anaplastic lymphoma kinase inhibitors. Current research is focused on combining targeted therapy with platinum-based chemotherapy in an endeavor to achieve an additional benefit in specific patient populations. Currently, pemetrexed is indicated for use in the first-line, maintenance, and second-line settings for the treatment of nonsquamous NSCLC. The combination of pemetrexed and cisplatin is well tolerated and is the approved standard first-line therapy. Thus, the pemetrexed-platinum backbone provides an attractive option for combination with targeted therapies. This review aims to summarize the current knowledge and future prospects of the use of pemetrexed-platinum as a backbone for combination with targeted therapies for NSCLC.

  3. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    NASA Astrophysics Data System (ADS)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  4. Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

    PubMed

    Duan, Li L; Gao, Ya; Mei, Ye; Zhang, Qing G; Tang, Bo; Zhang, John Z H

    2012-03-15

    Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure.

  5. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

    PubMed Central

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  6. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations.

    PubMed

    Liu, Qing; Shi, Chaowei; Yu, Lu; Zhang, Longhua; Xiong, Ying; Tian, Changlin

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner.

  7. Asymmetric synthesis of vinylogous β-amino acids and their incorporation into mixed backbone oligomers.

    PubMed

    Wu, Hao; An, Hongchan; Mo, Shuting Cynthia; Kodadek, Thomas

    2017-03-27

    Chiral vinylogous β-amino acids (VBAA) were synthesized using enantioselective Mannich reactions of aldehydes with in situ generated N-carbamoyl imines followed by a Horner-Wadsworth-Emmons reaction. The efficiency with which these units could be incorporated into oligomers with different moieties on the C- and N-terminal sides was established, as was the feasibility of sequencing oligomers containing VBAAs by tandem mass spectrometry. The data show that VBAAs will be useful building blocks for the construction of combinatorial libraries of peptidomimetic compounds.

  8. Constructive Criticism.

    ERIC Educational Resources Information Center

    Lieberfeld, Lawrence

    1982-01-01

    Many crucial questions need to be answered before a college embarks on a construction project and makes a substantial financial commitment. Computer modeling techniques can be used to make even complex project feasibility analyses. Available from Peat, Marwick, Mitchell & Co., 345 Park Avenue, New York, NY 10154. (MSE)

  9. Constructing Space

    NASA Astrophysics Data System (ADS)

    Henderson, Austin

    This chapter chronicles the growth of the author's understanding of Media Space through his 20-year experience with coupling spaces, using video. It is a “technology-first” understanding of the construction of space. Key ideas from research studies and practice are presented, and contrasts with other genres of communication are made. The implications for distributed collaboration are explored.

  10. Worldwide construction

    SciTech Connect

    Radler, M.

    1998-04-13

    Tables list major construction projects for refineries, petrochemical plants, sulfur plants, natural gas processing plants, and gas and oil pipelines. Data are compiled by country, company name, project type, added capacity, status of the project, expected completion date, contractor and contract type. Gas processes include LPG recovery, cryogenic separation, turboexpanders, LNG, liquefaction, desulfurization, NGL recovery, dehydration, hydrogen plants, and fractionators.

  11. Abstract Constructions.

    ERIC Educational Resources Information Center

    Pietropola, Anne

    1998-01-01

    Describes a lesson designed to culminate a year of eighth-grade art classes in which students explore elements of design and space by creating 3-D abstract constructions. Outlines the process of using foam board and markers to create various shapes and optical effects. (DSK)

  12. Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers

    NASA Astrophysics Data System (ADS)

    Roach, David J.; Dou, Shichen; Colby, Ralph H.; Mueller, Karl T.

    2013-05-01

    Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ˜x 1{.1} Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for the

  13. Solid State Nuclear Magnetic Resonance Investigation of Polymer Backbone Dynamics in Poly(Ethylene Oxide) Based Lithium and Sodium Polyether-ester-sulfonate Ionomers

    SciTech Connect

    Roach, David J.; Dou, Shichen; Colby, Ralph H.; Mueller, Karl T.

    2013-01-01

    Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ≳ 1.1 Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for

  14. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy.

    PubMed Central

    Ab, E.; Schuurman-Wolters, G. K.; Saier, M. H.; Reizer, J.; Jacuinod, M.; Roepstorff, P.; Dijkstra, K.; Scheek, R. M.; Robillard, G. T.

    1994-01-01

    The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. PMID:8003964

  15. Optimal synchronization in space.

    PubMed

    Brede, Markus

    2010-02-01

    In this Rapid Communication we investigate spatially constrained networks that realize optimal synchronization properties. After arguing that spatial constraints can be imposed by limiting the amount of "wire" available to connect nodes distributed in space, we use numerical optimization methods to construct networks that realize different trade offs between optimal synchronization and spatial constraints. Over a large range of parameters such optimal networks are found to have a link length distribution characterized by power-law tails P(l) proportional to l(-alpha), with exponents alpha increasing as the networks become more constrained in space. It is also shown that the optimal networks, which constitute a particular type of small world network, are characterized by the presence of nodes of distinctly larger than average degree around which long-distance links are centered.

  16. Optimal synchronization in space

    NASA Astrophysics Data System (ADS)

    Brede, Markus

    2010-02-01

    In this Rapid Communication we investigate spatially constrained networks that realize optimal synchronization properties. After arguing that spatial constraints can be imposed by limiting the amount of “wire” available to connect nodes distributed in space, we use numerical optimization methods to construct networks that realize different trade offs between optimal synchronization and spatial constraints. Over a large range of parameters such optimal networks are found to have a link length distribution characterized by power-law tails P(l)∝l-α , with exponents α increasing as the networks become more constrained in space. It is also shown that the optimal networks, which constitute a particular type of small world network, are characterized by the presence of nodes of distinctly larger than average degree around which long-distance links are centered.

  17. Sandwich construction

    NASA Astrophysics Data System (ADS)

    Marshall, A.

    A form of composites known as structural sandwich construction is presented in terms of materials used, design details for solving edging and attachment problems, and charts of design material analysis. Sandwich construction is used in nearly all commercial airliners and helicopters, and military air and space vehicles, and it is shown that this method can stiffen a structure without causing a weight increase. The facing material can be made of 2024 or 7075 aluminum alloy, titanium, or stainless steel, and the core material can be wood or foam. The properties of paper honeycomb and various aluminum alloy honeycombs are presented. Factors pertaining to adhesive materials are discussed, including products given off during cure, bonding pressure, and adaptability. Design requirements and manufacturing specifications are resolved using numerous suggestions.

  18. Airship construction

    NASA Technical Reports Server (NTRS)

    Roda, J.

    1975-01-01

    Forty-four years ago the first successful metal airship was completed and delivered to the United States Navy, the ZMC-2. Between those years and the present, very little effort or serious consideration has been given to the manufacture, design, construction, or economic impact of airships. It is important to retain and exploit the small but continually diminishing pool of airship talent that will expedite the success of the United States in what is now a pioneering venture. The relative simplicity of airship construction, utilizing the tremendous technical advances of the last 44 years, leads to the conclusion that this form of transportation holds great promise for reducing costs of military missions and improving the international competitive position of the United States in commercial applications.

  19. Constructing computer virus phylogenies

    SciTech Connect

    Goldberg, L.A.; Goldberg, P.W.; Phillips, C.A.; Sorkin, G.B.

    1996-03-01

    There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses--a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is ``invented`` only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimal number of edges. In general, this optimization problem cannot be solved in quasi-polynomial time unless NQP=QP; we present positive and negative results for associated approximated problems. When tree solutions exist, they can be constructed and randomly sampled in polynomial time.

  20. Constructive Engineering of Simulations

    NASA Technical Reports Server (NTRS)

    Snyder, Daniel R.; Barsness, Brendan

    2011-01-01

    Joint experimentation that investigates sensor optimization, re-tasking and management has far reaching implications for Department of Defense, Interagency and multinational partners. An adaption of traditional human in the loop (HITL) Modeling and Simulation (M&S) was one approach used to generate the findings necessary to derive and support these implications. Here an entity-based simulation was re-engineered to run on USJFCOM's High Performance Computer (HPC). The HPC was used to support the vast number of constructive runs necessary to produce statistically significant data in a timely manner. Then from the resulting sensitivity analysis, event designers blended the necessary visualization and decision making components into a synthetic environment for the HITL simulations trials. These trials focused on areas where human decision making had the greatest impact on the sensor investigations. Thus, this paper discusses how re-engineering existing M&S for constructive applications can positively influence the design of an associated HITL experiment.

  1. Construction measurements

    SciTech Connect

    Barry, B.A.

    1988-01-01

    This text/reference on construction measurements contains material concerning electronic surveying and remote sensing. New to this edition is coverage of the GPS satellite positioning system, electronic distance measurement (EDM), laser sweep, calculator techniques, radial surveying and tracking, Loran-C, inertial navigation surveying, 3-point resection, computer software, and electronic fieldbooks. It covers the difference of elevation, angle measurements and directions, coordinate surveying and layout, offshore measurements, and random field and office techniques.

  2. Optimizing Computer Technology Integration

    ERIC Educational Resources Information Center

    Dillon-Marable, Elizabeth; Valentine, Thomas

    2006-01-01

    The purpose of this study was to better understand what optimal computer technology integration looks like in adult basic skills education (ABSE). One question guided the research: How is computer technology integration best conceptualized and measured? The study used the Delphi method to map the construct of computer technology integration and…

  3. Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides

    NASA Technical Reports Server (NTRS)

    Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

    2001-01-01

    The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

  4. TACN-based cationic lipids with amino acid backbone and double tails: materials for non-viral gene delivery.

    PubMed

    Wang, Bing; Yi, Wen-Jing; Zhang, Ji; Zhang, Qin-Fang; Xun, Miao-Miao; Yu, Xiao-Qi

    2014-04-01

    Cationic lipids have become an efficient type of non-viral vectors for gene delivery. In this Letter, four cationic lipids containing 1,4,7-triazacyclononane (TACN) headgroup, glutamic/aspartic acid backbone and dioleyl tails were designed and synthesized. The TACN headgroup gives these lipids excellent pH buffering capacities, which were higher than branched 25 kDa PEI. Cationic liposomes prepared from these lipids and DOPE showed good DNA affinity, and full DNA condensation was found at N/P ratio of 3 via agarose gel electrophoresis. The lipoplexes were characterized by dynamic light scattering (DLS) assay, which gave proper particle sizes and zeta-potentials for transfection. In vitro gene transfection results in two cell lines reveal that TAN (with aspartic acid and amide bond in the structure) shows the best transfection efficiency, which is close to commercially available transfection agent Lipofectamine 2000.

  5. NMR Spectroscopic Assignment of Backbone and Side-Chain Protons in Fully Protonated Proteins: Microcrystals, Sedimented Assemblies, and Amyloid Fibrils.

    PubMed

    Stanek, Jan; Andreas, Loren B; Jaudzems, Kristaps; Cala, Diane; Lalli, Daniela; Bertarello, Andrea; Schubeis, Tobias; Akopjana, Inara; Kotelovica, Svetlana; Tars, Kaspars; Pica, Andrea; Leone, Serena; Picone, Delia; Xu, Zhi-Qiang; Dixon, Nicholas E; Martinez, Denis; Berbon, Mélanie; El Mammeri, Nadia; Noubhani, Abdelmajid; Saupe, Sven; Habenstein, Birgit; Loquet, Antoine; Pintacuda, Guido

    2016-12-12

    We demonstrate sensitive detection of alpha protons of fully protonated proteins by solid-state NMR spectroscopy with 100-111 kHz magic-angle spinning (MAS). The excellent resolution in the Cα-Hα plane is demonstrated for 5 proteins, including microcrystals, a sedimented complex, a capsid and amyloid fibrils. A set of 3D spectra based on a Cα-Hα detection block was developed and applied for the sequence-specific backbone and aliphatic side-chain resonance assignment using only 500 μg of sample. These developments accelerate structural studies of biomolecular assemblies available in submilligram quantities without the need of protein deuteration.

  6. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-07-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  7. Polysiloxane-backbone block copolymers in a one-pot synthesis: a silicone platform for facile functionalization.

    PubMed

    Boehm, Paul; Mondeshki, Mihail; Frey, Holger

    2012-11-14

    Block copolymers consisting exclusively of a silicon-oxygen backbone are synthesized by sequential anionic ring-opening polymerization of different cyclic siloxane monomers. After formation of a poly(dimethylsiloxane) (PDMS) block by butyllithium-initiated polymerization of D3, a functional second block is generated by subsequent addition of tetramethyl tetravinyl cyclotetrasiloxane (D4(V) ), resulting in diblock copolymers comprised a simple PDMS block and a functional poly(methylvinylsiloxane) (PMVS) block. Polymers of varying block length ratios were obtained and characterized. The vinyl groups of the second block can be easily modified with a variety of side chains using hydrosilylation chemistry to attach compounds with Si-H bond. Conversion of the hydrosilylation used for polymer modification was investigated.

  8. ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization.

    PubMed

    Fingerhut, Benjamin P; Oesterling, Sven; Haiser, Karin; Heil, Korbinian; Glas, Andreas; Schreier, Wolfgang J; Zinth, Wolfgang; Carell, Thomas; de Vivie-Riedle, Regina

    2012-05-28

    Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

  9. ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

    NASA Astrophysics Data System (ADS)

    Fingerhut, Benjamin P.; Oesterling, Sven; Haiser, Karin; Heil, Korbinian; Glas, Andreas; Schreier, Wolfgang J.; Zinth, Wolfgang; Carell, Thomas; de Vivie-Riedle, Regina

    2012-05-01

    Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

  10. Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail).

    PubMed

    Plan, Manuel Rey R; Saska, Ivana; Cagauan, Arsenia G; Craik, David J

    2008-07-09

    Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides.

  11. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    PubMed

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  12. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  13. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    PubMed Central

    Marassi, Francesca M.; Ding, Yi; Schwieters, Charles D.; Tian, Ye; Yao, Yong

    2015-01-01

    SUMMARY The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential. PMID:26143069

  14. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy

    PubMed Central

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2015-01-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm−1 maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841

  15. Directed evolution of a sphingomyelin flippase reveals mechanism of substrate backbone discrimination by a P4-ATPase

    PubMed Central

    Graham, Todd R.

    2016-01-01

    Phospholipid flippases in the type IV P-type ATPase (P4-ATPases) family establish membrane asymmetry and play critical roles in vesicular transport, cell polarity, signal transduction, and neurologic development. All characterized P4-ATPases flip glycerophospholipids across the bilayer to the cytosolic leaflet of the membrane, but how these enzymes distinguish glycerophospholipids from sphingolipids is not known. We used a directed evolution approach to examine the molecular mechanisms through which P4-ATPases discriminate substrate backbone. A mutagenesis screen in the yeast Saccharomyces cerevisiae has identified several gain-of-function mutations in the P4-ATPase Dnf1 that facilitate the transport of a novel lipid substrate, sphingomyelin. We found that a highly conserved asparagine (N220) in the first transmembrane segment is a key enforcer of glycerophospholipid selection, and specific substitutions at this site allow transport of sphingomyelin. PMID:27432949

  16. Backbone resonance assignments for the PHD-Bromo dual-domain of the human chromatin reader TRIM24.

    PubMed

    Walser, Reto; Renshaw, Jonathan; Milbradt, Alexander G

    2016-04-01

    Plant homeodomains (PHD) and Bromo domains are both chromatin reader domains that recognise histone methylation degree and acetylation state, respectively. The tripartite motif protein TRIM24 is a multidomain protein carrying a PHD-Bromo motif at its C-terminus, through which it is able to bind to histone 3 (H3) N-terminal tails with a specific modification pattern, namely unmethylated at K4 and acetylated at K23 (H3-K4me0K23ac). Here we report the 1H, 13C and 15N backbone resonance assignment of this 23 kDa motif, which we have obtained by heteronuclear multidimensional NMR spectroscopy. Furthermore we show that the secondary Cα and Cβ chemical shifts are in good agreement with a previously published crystal structure.

  17. Positive Psychologists on Positive Constructs

    ERIC Educational Resources Information Center

    Lyubomirsky, Sonja

    2012-01-01

    Comments on the original article by McNulty and Fincham (see record 2011-15476-001). In their article, the authors offered compelling evidence that constructs such as forgiveness and optimism can have both beneficial and adverse consequences, depending on the context. Their caution about labeling particular psychological processes as "positive" is…

  18. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

    PubMed

    Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

    2015-05-12

    Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

  19. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  20. Anatomy as the backbone of an integrated first year medical curriculum: design and implementation.

    PubMed

    Klement, Brenda J; Paulsen, Douglas F; Wineski, Lawrence E

    2011-01-01

    Morehouse School of Medicine chose to restructure its first year medical curriculum in 2005. The anatomy faculty had prior experience in integrating courses, stemming from the successful integration of individual anatomical sciences courses into a single course called Human Morphology. The integration process was expanded to include the other first year basic science courses (Biochemistry, Physiology, and Neurobiology) as we progressed toward an integrated curriculum. A team, consisting of the course directors, a curriculum coordinator, and the Associate Dean for Educational and Faculty Affairs, was assembled to build the new curriculum. For the initial phase, the original course titles were retained but the lecture order was reorganized around the Human Morphology topic sequence. The material from all four courses was organized into four sequential units. Other curricular changes included placing laboratories and lectures more consistently in the daily routine, reducing lecture time from 120 to 90 minute blocks, eliminating unnecessary duplication of content, and increasing the amount of independent study time. Examinations were constructed to include questions from all courses on a single test, reducing the number of examination days in each block from three to one. The entire restructuring process took two years to complete, and the revised curriculum was implemented for the students entering in 2007. The outcomes of the restructured curriculum include a reduction in the number of contact hours by 28%, higher or equivalent subject examination average scores, enhanced student satisfaction, and a first year curriculum team better prepared to move forward with future integration.

  1. Controlled conjugated backbone twisting for an increased open-circuit voltage while having a high short-circuit current in poly(hexylthiophene) derivatives.

    PubMed

    Ko, Sangwon; Hoke, Eric T; Pandey, Laxman; Hong, Sanghyun; Mondal, Rajib; Risko, Chad; Yi, Yuanping; Noriega, Rodrigo; McGehee, Michael D; Brédas, Jean-Luc; Salleo, Alberto; Bao, Zhenan

    2012-03-21

    Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone--due to an increase in the polymer ionization potential--while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2':5',2''-terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C(71)-butyric acid methyl ester (PC(71)BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current.

  2. Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism

    PubMed Central

    Bale, Shridhar; Halfmann, Peter; Zandonatti, Michelle A.; Kunert, John; Kroon, Gerard J. A.; Kawaoka, Yoshihiro; MacRae, Ian J.; Wilson, Ian A.; Saphire, Erica Ollmann

    2012-01-01

    Filoviruses, including Marburg virus (MARV) and Ebola virus (EBOV), cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (ds)RNA-binding domain (RBD) of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules. PMID:23028316

  3. Lactobacillus rhamnosus accelerates zebrafish backbone calcification and gonadal differentiation through effects on the GnRH and IGF systems.

    PubMed

    Avella, Matteo A; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

    2012-01-01

    Endogenous microbiota play essential roles in the host's immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host's development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application.

  4. Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

    PubMed

    Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

    2015-03-10

    Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

  5. Lactobacillus rhamnosus Accelerates Zebrafish Backbone Calcification and Gonadal Differentiation through Effects on the GnRH and IGF Systems

    PubMed Central

    Avella, Matteo A.; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

    2012-01-01

    Endogenous microbiota play essential roles in the host’s immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host’s development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application. PMID:23029107

  6. Photomodulation of conformational states. I. Mono- and bicyclic peptides with (4-amino)phenylazobenzoic acid as backbone constituent.

    PubMed

    Renner, C; Behrendt, R; Spörlein, S; Wachtveitl, J; Moroder, L

    2000-12-01

    The thioredoxin reductase active-site fragment H-Ala-Cys-Ala-Thr-Cys-Asp-Gly-Phe-OH [134-141], which is known for its high tendency to assume an almost identical conformation as in the intact enzyme, was backbone cyclized with the photoresponsive (4-amino)phenylazobenzoic acid (APB) to produce a monocyclic and disulfide-bridged bicyclic APB-peptide. Light-induced reversible cis/trans isomerization occurs at identical extents in both the linear and the two cyclic forms. Nuclear magnetic resonance conformational analysis clearly revealed that in the bicyclic APB-peptide both as a trans- and cis-azo-isomer the constraints imparted by the bicyclic structure do not allow the molecule to relax into a defined low energy conformation, thus making the molecule a frustrated system that flip-flops between multiple conformational states. Conversely, the monocyclic APB peptide folds into a well-defined lowest energy structure as a trans-azo-isomer, which upon photoisomerization to the cis-azo configuration relaxes into a less restricted conformational space. First femtosecond spectroscopic analysis of the dynamics of the photoreaction confirm a fast first phase on the femtosecond time scale related to the cis/trans isomerization of the azobenzene moiety followed by a slower phase in the picosecond time scale that involves an adjustment of the peptide backbone. Due to the well- defined photoresponsive two-state transition of this monocyclic peptide molecule, it represents a model system well suited for studying the ultrafast dynamics of conformational transitions by time-resolved spectroscopy.

  7. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

    PubMed

    Reddy, Jithender G; Hosur, Ramakrishna V

    2014-03-01

    Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.

  8. Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic archaeon Pyrococcus furiosus.

    PubMed Central

    Peak, M J; Robb, F T; Peak, J G

    1995-01-01

    Pyrococcus furiosus is a hyperthermophilic archaeon that grows optimally at 100 degrees C. It is not conceivable that these organisms could survive with genomic DNA that was subject to thermal destruction, yet the mechanisms protecting the genomes of this and other hyperthermophiles against such destruction are obscure. We have determined the effect of elevated temperatures up to 110 degrees C on the molecular weight of DNA in intact P. furiosus cells, compared with the effect of elevated temperatures on DNA in the mesothermophilic bacterium Escherichia coli. At 100 degrees C, DNA in P. furiosus cells is about 20 times more resistant to thermal breakage than that in E. coli cells, and six times fewer breaks were found in P. furiosus DNA after exposure to 110 degrees C for 30 min than in E. coli DNA at 95 degrees C. Our hypothesis for this remarkable stability of DNA in a hyperthermophile is that this hyperthermophile possesses DNA-binding proteins that protect against hydrolytic damage, as well as other endogenous protective mechanisms and DNA repair enzyme systems. PMID:7592404

  9. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by 15N NMR relaxation methods.

    PubMed

    Canales-Mayordomo, Angeles; Fayos, Rosa; Angulo, Jesús; Ojeda, Rafael; Martín-Pastor, Manuel; Nieto, Pedro M; Martín-Lomas, Manuel; Lozano, Rosa; Giménez-Gallego, Guillermo; Jiménez-Barbero, Jesús

    2006-08-01

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR).

  10. Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging

    PubMed Central

    Guo, Jia; Wang, Shenliang; Dai, Nan; Teo, Yin Nah; Kool, Eric T.

    2011-01-01

    Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410–670 nm. We developed a new approach to antibody conjugation, using Huisgen–Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340–380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time. PMID:21321224

  11. PUMP CONSTRUCTION

    DOEpatents

    Strickland, G.; Horn, F.L.; White, H.T.

    1960-09-27

    A pump which utilizes the fluid being pumped through it as its lubricating fluid is described. This is achieved by means of an improved bearing construction in a pump of the enclosed or canned rotor type. At the outlet end of the pump, adjacent to an impeller mechanism, there is a bypass which conveys some of the pumped fluid to a chamber at the inlet end of the pump. After this chamber becomes full, the pumped fluid passes through fixed orifices in the top of the chamber and exerts a thrust on the inlet end of the pump rotor. Lubrication of the rotor shaft is accomplished by passing the pumped fluid through a bypass at the outlet end of the rotor shaft. This bypass conveys Pumped fluid to a cooling means and then to grooves on the surface of the rotor shait, thus lubricating the shaft.

  12. Constructing Knowledge

    NASA Astrophysics Data System (ADS)

    Blanton, Patricia

    2003-02-01

    Schools are expected to lay the foundation upon which knowledge can be built and equip students with the tools necessary to accomplish the construction. The role of the teacher in this building process is crucial to the type of structure the student can build. Whether you call it constructivism, discussion teaching, project-based learning, inquiry learning, or any of the other names given to the instructional strategies being suggested by education researchers, the key is getting students to become active participants in the process. While some students may be able to learn from eloquently delivered lectures and dynamic demonstrations, the majority of students cannot effectively retain and apply ideas communicated in this manner.

  13. Facile Construction of Random Gene Mutagenesis Library for Directed Evolution Without the Use of Restriction Enzyme in Escherichia coli.

    PubMed

    Kim, Jae-Eung; Huang, Rui; Chen, Hui; You, Chun; Zhang, Y-H Percival

    2016-09-01

    A foolproof protocol was developed for the construction of mutant DNA library for directed protein evolution. First, a library of linear mutant gene was generated by error-prone PCR or molecular shuffling, and a linear vector backbone was prepared by high-fidelity PCR. Second, the amplified insert and vector fragments were assembled by overlap-extension PCR with a pair of 5'-phosphorylated primers. Third, full-length linear plasmids with phosphorylated 5'-ends were self-ligated with T4 ligase, yielding circular plasmids encoding mutant variants suitable for high-efficiency transformation. Self-made competent Escherichia coli BL21(DE3) showed a transformation efficiency of 2.4 × 10(5) cfu/µg of the self-ligated circular plasmid. Using this method, three mutants of mCherry fluorescent protein were found to alter their colors and fluorescent intensities under visible and UV lights, respectively. Also, one mutant of 6-phosphorogluconate dehydrogenase from a thermophilic bacterium Moorella thermoacetica was found to show the 3.5-fold improved catalytic efficiency (kcat /Km ) on NAD(+) as compared to the wild-type. This protocol is DNA-sequence independent, and does not require restriction enzymes, special E. coli host, or labor-intensive optimization. In addition, this protocol can be used for subcloning the relatively long DNA sequences into any position of plasmids.

  14. Backbone assignments and secondary structure of the Escherichia coli enzyme-II mannitol A domain determined by heteronuclear three-dimensional NMR spectroscopy.

    PubMed Central

    Kroon, G. J.; Grötzinger, J.; Dijkstra, K.; Scheek, R. M.; Robillard, G. T.

    1993-01-01

    This report presents the backbone assignments and the secondary structure determination of the A domain of the Escherichia coli mannitol transport protein, enzyme-IImtl. The backbone resonances were partially assigned using three-dimensional heteronuclear 1H NOE 1H-15N single-quantum coherence (15N NOESY-HSQC) spectroscopy and three-dimensional heteronuclear 1H total correlation 1H-15N single-quantum coherence (15N TOCSY-HSQC) spectroscopy on uniformly 15N enriched protein. Triple-resonance experiments on uniformly 15N/13C enriched protein were necessary to complete the backbone assignments, due to overlapping 1H and 15N frequencies. Data obtained from three-dimensional 1H-15N-13C alpha correlation experiments (HNCA and HN(CO)CA), a three-dimensional 1H-15N-13CO correlation experiment (HNCO), and a three-dimensional 1H alpha-13C alpha-13CO correlation experiment (COCAH) were combined using SNARF software, and yielded the assignments of virtually all observed backbone resonances. Determination of the secondary structure of IIAmtl is based upon NOE information from the 15N NOESY-HSQC and the 1H alpha and 13C alpha secondary chemical shifts. The resulting secondary structure is considerably different from that reported for IIAglc of E. coli and Bacillus subtilis determined by NMR and X-ray. PMID:8401218

  15. Live virus vaccines based on a yellow fever vaccine backbone: standardized template with key considerations for a risk/benefit assessment.

    PubMed

    Monath, Thomas P; Seligman, Stephen J; Robertson, James S; Guy, Bruno; Hayes, Edward B; Condit, Richard C; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

    2015-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called "chimeric virus vaccines"). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus, Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were exchanged for the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of

  16. Live Virus Vaccines Based on a Yellow Fever Vaccine Backbone: Standardized Template with Key Considerations for a Risk/Benefit Assessment*

    PubMed Central

    Monath, Thomas P.; Seligman, Stephen J.; Robertson, James S.; Guy, Bruno; Hayes, Edward B.; Condit, Richard C.; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

    2015-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called “chimeric virus vaccines”). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were replaced by the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of

  17. Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance

    NASA Astrophysics Data System (ADS)

    Eles, Philip Thomas

    2005-07-01

    In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necess-itating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent frac-tion of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and

  18. Constructing ecologies.

    PubMed

    Cropp, Roger; Norbury, John

    2012-02-07

    We synthesize the generic properties of ecologically realistic multi-trophic level models and define criteria for ecological realism. We define an "ecospace" in which all ecologically realistic dynamics are confined, and construct "resource rays" that define the resources available to each species at every point in the ecospace. Resource rays for a species are lines from a vertex of maximum resource to the opposite boundary where no resources are available. The growth functions of all biota normally decrease along their resource rays, and change sign from positive to negative. This property prescribes that each species must have a zero isosurface within the ecospace. We illustrate our conditions on a highly cited three trophic level model from population dynamics, showing how to extend this system biologically consistently to a closed ecological system. Our synthesis extends the concept of carrying capacity of population models to explicitly include exhaustion of limiting resources, and so allows for population biology models to be considered as ecologically closed systems with respect to a key limiting nutrient. This approach unifies many theoretical and applied models in a common biogeochemical framework, facilitates better understanding of the key structures of complex ecologies, and suggests strategies for efficient design of experiments.

  19. Constructing Brambles

    NASA Astrophysics Data System (ADS)

    Chapelle, Mathieu; Mazoit, Frédéric; Todinca, Ioan

    Given an arbitrary graph G and a number k, it is well-known by a result of Seymour and Thomas [22] that G has treewidth strictly larger than k if and only if it has a bramble of order k + 2. Brambles are used in combinatorics as certificates proving that the treewidth of a graph is large. From an algorithmic point of view there are several algorithms computing tree-decompositions of G of width at most k, if such decompositions exist and the running time is polynomial for constant k. Nevertheless, when the treewidth of the input graph is larger than k, to our knowledge there is no algorithm constructing a bramble of order k + 2. We give here such an algorithm, running in {mathcal O}(n^{k+4}) time. For classes of graphs with polynomial number of minimal separators, we define a notion of compact brambles and show how to compute compact brambles of order k + 2 in polynomial time, not depending on k.

  20. Construction research

    SciTech Connect

    1994-12-31

    The papers in this volume report information on fast-track paving, statistically based specifications, bridge rehabilitation, contracts management, and automation in hot in-place asphalt pavement recycling. Hossain and Wojakowski discuss the construction and performance of a fast-track concrete pavement in Kansas. Weed presents the use of composite pay equations as a means of eliminating the confusion and difficulty in administering the acceptance testing of various quality characteristics. He uses an example based on portland cement concrete pavement to illustrate the practicality of this method. Taavoni describes the upgrading and recycling of an 1879 wrought-iron pin connected truss bridge by replacing the pins. Abdul-Malak and Abou-Assaly investigate innovative concepts of contract management to improve the execution of contracts in Lebanon. They present an integrated contract management approach directed toward understanding the interactions, interrelationships, and interdependencies that exist among candidate concepts and strategies. Pagdadis and Ishai discuss the use of automated equipment used for hot in-place asphalt resurfacing and the breakthroughs that have been achieved toward improving this particular site process through real-time data handling.

  1. N-H stretching modes around 3300 wavenumber from peptide backbones observed by chiral sum frequency generation vibrational spectroscopy.

    PubMed

    Fu, Li; Wang, Zhuguang; Yan, Elsa C Y

    2014-09-01

    We present a detailed analysis of the molecular origin of the chiral sum frequency generation (SFG) signals of proteins and peptides at interfaces in the N-H stretching vibrational region. The N-H stretching can be a probe for investigating structural and functional properties of proteins, but remains technically difficult to analyze due to the overlapping with the O-H stretching of water molecules. Chiral SFG spectroscopy offers unique tools to study the N-H stretching from proteins at interfaces without interference from the water background. However, the molecular origin of the N-H stretching signals of proteins is still unclear. This work provides a justification of the origin of chiral N-H signals by analyzing the vibrational frequencies, examining chiral SFG theory, studying proton (hydrogen/deuterium) exchange kinetics, and performing optical control experiments. The results demonstrate that the chiral N-H stretching signals at ~3300 cm(-1) originate from the amide group of the protein backbones. This chiral N-H stretching signal offers an in situ, real-time, and background-free probe for interrogating the protein structures and dynamics at interfaces at the molecular level.

  2. Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

    NASA Astrophysics Data System (ADS)

    Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

    2016-12-01

    The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB.

  3. High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone.

    PubMed

    Saxena, Saurabh; Stanek, Jan; Cevec, Mirko; Plavec, Janez; Koźmiński, Wiktor

    2015-11-01

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of (1)H and (13)C chemical shifts, especially of C4'/H4'. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4'-H4' correlations are resolved along the (1)H3'-(31)P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional (31)P and (1)H3' dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic (13)C-labeling with evolution of C4' carbons. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4'-C3' and C4'-C5' homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  4. Signal amplification in immunohistochemistry: loose-jointed deformable heteropolymeric HRP conjugates vs. linear polymer backbone HRP conjugates.

    PubMed

    Buchwalow, Igor; Boecker, Werner; Wolf, Eduard; Samoilova, Vera; Tiemann, Markus

    2013-07-01

    Improvements in reagents and protocols for immunohistochemistry have led to increased sensitivity of detection systems. A significant level of signal amplification was achieved by the chain-polymer conjugate technology utilizing enzyme-labeled inert "backbone" molecule of dextran (Dako). However, the relatively large size of the dextran molecule in aqueous phase appears to create spatial hindrance compromising the penetrative ability of the detection reagent. Novel AmpliStain™ detection systems (SDT GmbH, Baesweiler, Germany) seem to overcome these constraints offering a more compact and deformable conjugate design that facilitates agile penetration through the narrowest diffusion pathways in tissue sections. Here, we compared the level of signal amplification achievable with AmpliStain™-HRP (SDT) and EnVision™+-HRP (Dako). Our results show that the AmpliStain™-HRP systems allow higher dilutions of primary antibodies in both immunohistochemistry and ELISA. Compared with EnVision™+, anti-mouse AmpliStain™ enables at least three times more sensitive detection of mouse antibodies, whereas anti-rabbit AmpliStain™ is ten times more sensitive than anti-rabbit EnVision™+.

  5. Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

    PubMed Central

    Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

    2016-01-01

    The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB. PMID:27958362

  6. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    PubMed

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  7. Covalently Connecting Crystal Grains with Polyvinylammonium Carbochain Backbone To Suppress Grain Boundaries for Long-Term Stable Perovskite Solar Cells.

    PubMed

    Li, Han; Liang, Chao; Liu, Yingliang; Zhang, Yiqiang; Tong, Jincheng; Zuo, Weiwei; Xu, Shengang; Shao, Guosheng; Cao, Shaokui

    2017-02-22

    Grain boundaries act as rapid pathways for nonradiative carrier recombination, anion migration, and water corrosion, leading to low efficiency and poor stability of organometal halide perovskite solar cells (PSCs). In this work, the strategy suppressing the crystal grain boundaries is applied to improve the photovoltaic performance, especially moisture-resistant stability, with polyvinylammonium carbochain backbone covalently connecting the perovskite crystal grains. This cationic polyelectrolyte additive serves as nucleation sites and template for crystal growth of MAPbI3 and afterward the immobilized adjacent crystal grains grow into the continuous compact, pinhole-free perovskite layer. As a result, the unsealed PSC devices, which are fabricated under low-temperature fabrication protocol with a proper content of polymer additive PVAm·HI, currently exhibit the maximum efficiency of 16.3%. Remarkably, these unsealed devices follow an "outside-in" corrosion mechanism and respectively retain 92% and 80% of the initial PCE value after being exposed under ambient environment for 50 days and 100 days, indicating the superiority of carbochain polymer additives in solving the long-term stability problem of PSCs.

  8. Bilayer surface association of the pHLIP peptide promotes extensive backbone desolvation and helically-constrained structures.

    PubMed

    Brown, Mia C; Yakubu, Rauta A; Taylor, Jay; Halsey, Christopher M; Xiong, Jian; Jiji, Renee D; Cooley, Jason W

    2014-01-01

    Despite their presence in many aspects of biology, the study of membrane proteins lags behind that of their soluble counterparts. Improving structural analysis of membrane proteins is essential. Deep-UV resonance Raman (DUVRR) spectroscopy is an emerging technique in this area and has demonstrated sensitivity to subtle structural transitions and changes in protein environment. The pH low insertion peptide (pHLIP) has three distinct structural states: disordered in an aqueous environment, partially folded and associated with a lipid membrane, and inserted into a lipid bilayer as a transmembrane helix. While the soluble and membrane-inserted forms are well characterized, the partially folded membrane-associated state has not yet been clearly described. The amide I mode, known to be sensitive to protein environment, is the same in spectra of membrane-associated and membrane-inserted pHLIP, indicating comparable levels of backbone dehydration. The amide S mode, sensitive to helical structure, indicates less helical character in the membrane-associated form compared to the membrane-inserted state, consistent with previous findings. However, the structurally sensitive amide III region is very similar in both membrane-associated and membrane-inserted pHLIP, suggesting that the membrane-associated form has a large amount of ordered structure. Where before the membrane-associated state was thought to contain mostly unordered structure and reside in a predominantly aqueous environment, we have shown that it contains a significant amount of ordered structure and rests deeper within the lipid membrane.

  9. Aminoacyl-tRNA Substrate and Enzyme Backbone Atoms Contribute to Translational Quality Control by YbaK

    PubMed Central

    Kumar, Sandeep; Das, Mom; Hadad, Christopher M.; Musier-Forsyth, Karin

    2012-01-01

    Amino acids are covalently attached to their corresponding tRNAs by aminoacyl-tRNA synthetases. Proofreading mechanisms exist to ensure that high fidelity is maintained in this key step in protein synthesis. Prolyl-tRNA synthetase (ProRS) can misacylate cognate tRNAPro with Ala and Cys. The cis-editing domain of ProRS (INS) hydrolyzes Ala-tRNAPro, whereas Cys-tRNAPro is hydrolyzed by a single domain editing protein, YbaK, in trans. Previous studies have proposed a model of substrate-binding by bacterial YbaK and elucidated a substrate-assisted mechanism of catalysis. However, the microscopic steps in this mechanism have not been investigated. In this work, we carried out biochemical experiments together with a detailed hybrid quantum mechanics/molecular mechanics study to investigate the mechanism of catalysis by Escherichia coli YbaK. The results support a mechanism wherein cyclization of the substrate Cys results in cleavage of the Cys-tRNA ester bond. Protein side chains do not play a significant role in YbaK catalysis. Instead, protein backbone atoms play crucial roles in stabilizing the transition state, while the product is stabilized by the 2'-OH of the tRNA. PMID:23185990

  10. Management of Adolescent Low-Risk Classical Hodgkin Lymphoma: Which Chemotherapy Backbone Gives the Best Chance of Omitting Radiotherapy Safely.

    PubMed

    Algiraigri, Ali H; Essa, Mohammed F

    2016-03-01

    Even though more than 90% of adolescents with low-risk classical Hodgkin lymphoma (LRcHL) will be cured with first-line therapy, many will suffer serious late toxic effects from radiotherapy (RT). The goals for care have shifted toward minimizing late toxic effects without compromising the outstanding cure rates by adapting a risk and response-based therapy. Recent published and ongoing randomized clinical trials, using functional imaging, may allow for better identification of those patients for whom RT may be safely omitted while maintaining excellent cure rates. To evaluate the best chemotherapy regimens with a reasonable toxicity profile and that are expected to have a high chance of omitting RT based on a response-directed therapy while maintaining high cure rates, a mini review was conducted of the recent clinical trials in pediatric and adult LRcHL. The UK RAPID trial chemotherapy backbone (3 × ABVD) followed by a response-based positron emission tomography scan offers up to a 75% chance of safely omitting RT without compromising the cure rate, which remained well above 90%.

  11. Impairment assessment of orthogonal frequency division multiplexing over dispersion-managed links in backbone and backhaul networks

    NASA Astrophysics Data System (ADS)

    Tamilarasan, Ilavarasan; Saminathan, Brindha; Murugappan, Meenakshi

    2016-04-01

    The past decade has seen the phenomenal usage of orthogonal frequency division multiplexing (OFDM) in the wired as well as wireless communication domains, and it is also proposed in the literature as a future proof technique for the implementation of flexible resource allocation in cognitive optical networks. Fiber impairment assessment and adaptive compensation becomes critical in such implementations. A comprehensive analytical model for impairments in OFDM-based fiber links is developed. The proposed model includes the combined impact of laser phase fluctuations, fiber dispersion, self phase modulation, cross phase modulation, four-wave mixing, the nonlinear phase noise due to the interaction of amplified spontaneous emission with fiber nonlinearities, and the photodetector noises. The bit error rate expression for the proposed model is derived based on error vector magnitude estimation. The performance analysis of the proposed model is presented and compared for dispersion compensated and uncompensated backbone/backhaul links. The results suggest that OFDM would perform better for uncompensated links than the compensated links due to the negligible FWM effects and there is a need for flexible compensation. The proposed model can be employed in cognitive optical networks for accurate assessment of fiber-related impairments.

  12. High accuracy of Karplus equations for relating three-bond J couplings to protein backbone torsion angles.

    PubMed

    Li, Fang; Lee, Jung Ho; Grishaev, Alexander; Ying, Jinfa; Bax, Ad

    2015-02-23

    (3) JC'C' and (3) JHNHα couplings are related to the intervening backbone torsion angle ${\\varphi }$ by standard Karplus equations. Although these couplings are known to be affected by parameters other than ${\\varphi }$, including H-bonding, valence angles and residue type, experimental results and quantum calculations indicate that the impact of these latter parameters is typically very small. The solution NMR structure of protein GB3, newly refined by using extensive sets of residual dipolar couplings, yields 50-60 % better Karplus equation agreement between ${\\varphi }$ angles and experimental (3) JC'C' and (3) JHNHα values than does the high-resolution X-ray structure. In intrinsically disordered proteins, (3) JC'C' and (3) JHNHα couplings can be measured at even higher accuracy, and the impact of factors other than the intervening torsion angle on (3) J will be smaller than in folded proteins, making these couplings exceptionally valuable reporters on the ensemble of ${\\varphi }$ angles sampled by each residue.

  13. Structure of the exceptionally large nonrepetitive carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-82164.

    PubMed

    Vinogradov, Evgeny; Petersen, Bent O; Sadovskaya, Irina; Jabbouri, Said; Duus, Jens Ø; Helander, Ilkka M

    2003-07-01

    The structures of the oligosaccharides obtained after acetic acid hydrolysis and alkaline deacylation of the rough-type lipopolysaccharide (LPS) from Pectinatus frisingensis strain VTT E-82164 were analysed using NMR spectroscopy, MS and chemical methods. The LPS contains two major structural variants, differing by a decasaccharide fragment, and some minor variants lacking the terminal glucose residue. The largest structure of the carbohydrate backbone of the LPS that could be deduced from experimental results consists of 25 monosaccharides (including the previously found Ara4NP residue in lipid A) arranged in a well-defined nonrepetitive structure: We presume that the shorter variant with R1 = H represents the core-lipid A part of the LPS, and the additional fragment is present instead of the O-specific polysaccharide. Structures of this type have not been previously described. Analysis of the deacylation products obtained from the LPS of the smooth strain, VTT E-79100T, showed that it contains a very similar core but with one different glycosidic linkage.

  14. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  15. Backbone resonance assignments of an artificially engineered TEM-1/PSE-4 Class A β-lactamase chimera.

    PubMed

    Morin, Sébastien; Clouthier, Christopher M; Gobeil, Sophie; Pelletier, Joelle N; Gagné, Stéphane M

    2010-10-01

    The rapid evolution of Class A β-lactamases, which procure resistance to an increasingly broad panel of β-lactam antibiotics, underscores the urgency to better understand the relation between their sequence variation and their structural and functional features. To date, more than 300 clinically-relevant β-lactamase variants have been reported, and this number continues to increase. With the aim of obtaining insights into the evolutionary potential of β-lactamases, an artificially engineered, catalytically active chimera of the Class A TEM-1 and PSE-4 β-lactamases is under study by kinetics and NMR. Here we report the (1)H, (13)C and (15)N backbone resonance assignments for the 30 kDa chimera cTEM-17m. Despite its high molecular weight, the data provide evidence that this artificially-evolved chimeric enzyme is well folded. The hydrolytic activity of cTEM-17m was determined using the chromogenic substrate CENTA, with K (M) = 160 ± 35 μM and k (cat) = 20 ± 4 s(-1), which is in the same range as the values for TEM-1 and PSE-4 β-lactamases.

  16. Optimizing Locomotion

    NASA Astrophysics Data System (ADS)

    Hosoi, Anette

    2006-11-01

    In this talk we will discuss two optimization topics related to low Reynolds number locomotion: optimal stroke patterns in linked swimmers and optimal fluid material properties in adhesive locomotion. In contrast to many optimization problems, we do not consider geometry, rather we optimize the swimming kinematics or fluid material properties for a given geometrical configuration. In the first case, we begin by optimizing stroke patterns for Purcell's 3-link swimmer. We model the swimmer as a jointed chain of three slender links moving in an inertialess flow. The swimmer is optimized for both efficiency and speed. In the second case, we analyze the adhesive locomotion used by common gastropods such as snails and slugs. Such organisms crawl on a solid substrate by propagating muscular waves of shear stress on a viscoelastic mucus. Using a simple mechanical model, we derive criteria for favorable fluid material properties to lower the energetic cost of locomotion.

  17. RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation.

    PubMed

    Weichenrieder, Oliver

    2014-01-01

    The eukaryotic Sm and the Sm-like (LSm) proteins form a large family that includes LSm proteins in archaea and the Hfq proteins in bacteria. Commonly referred to as the (L)Sm protein family, the various members play important roles in RNA processing, decay, and riboregulation. Particularly interesting from a structural point of view is their ability to assemble into doughnut-shaped rings, which allows them to bind preferentially the uridine-rich 3'-end of RNA oligonucleotides. With an emphasis on Hfq, this review compares the RNA-binding properties of the various (L)Sm rings that were recently co-crystallized with RNA substrates, and it discusses how these properties relate to physiological function.

  18. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

    PubMed

    Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

    2014-01-14

    Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the

  19. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.

    PubMed

    Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří

    2013-05-21

    The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as

  20. Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments

    PubMed Central

    Lee, Wonbae; von Hippel, Peter H.; Marcus, Andrew H.

    2014-01-01

    DNA constructs labeled with cyanine fluorescent dyes are important substrates for single-molecule (sm) studies of the functional activity of protein–DNA complexes. We previously studied the local DNA backbone fluctuations of replication fork and primer–template DNA constructs labeled with Cy3/Cy5 donor–acceptor Förster resonance energy transfer (FRET) chromophore pairs and showed that, contrary to dyes linked ‘externally’ to the bases with flexible tethers, direct ‘internal’ (and rigid) insertion of the chromophores into the sugar-phosphate backbones resulted in DNA constructs that could be used to study intrinsic and protein-induced DNA backbone fluctuations by both smFRET and sm Fluorescent Linear Dichroism (smFLD). Here we show that these rigidly inserted Cy3/Cy5 chromophores also exhibit two additional useful properties, showing both high photo-stability and minimal effects on the local thermodynamic stability of the DNA constructs. The increased photo-stability of the internal labels significantly reduces the proportion of false positive smFRET conversion ‘background’ signals, thereby simplifying interpretations of both smFRET and smFLD experiments, while the decreased effects of the internal probes on local thermodynamic stability also make fluctuations sensed by these probes more representative of the unperturbed DNA structure. We suggest that internal probe labeling may be useful in studies of many DNA–protein interaction systems. PMID:24627223

  1. Generation of an optimized lentiviral vector encoding a high-expression factor VIII transgene for gene therapy of hemophilia A.

    PubMed

    Johnston, J M; Denning, G; Doering, C B; Spencer, H T

    2013-06-01

    We previously compared the expression of several human factor VIII (fVIII) transgene variants and demonstrated the superior expression properties of B domain-deleted porcine fVIII. Subsequently, a hybrid human/porcine fVIII molecule (HP-fVIII) comprising 91% human amino-acid sequence was engineered to maintain the high-expression characteristics of porcine fVIII. The bioengineered construct then was used effectively to treat knockout mice with hemophilia A. In the current study, we focused on optimizing self-inactivating (SIN) lentiviral vector systems by analyzing the efficacy of various lentiviral components in terms of virus production, transduction efficiency and transgene expression. Specifically, three parameters were evaluated: (1) the woodchuck hepatitis post-transcriptional regulatory element (WPRE), (2) HIV versus SIV viral vector systems and (3) various internal promoters. The inclusion of a WPRE sequence had negligible effects on viral production and HP-fVIII expression. HIV and SIV vectors were compared and found to be similar with respect to transduction efficiency in both K562s and HEK-293T cells. However, there was an enhanced expression of HP-fVIII by the SIV system, which was evident in both K562 and BHK-M cell lines. To further compare expression of HP-fVIII from an SIV-based lentiviral system, we constructed expression vectors containing the high expression transgene and a human elongation factor-1 alpha, cytomegalovirus (CMV) or phosphoglycerate kinase promoter. Expression was significantly greater from the CMV promoter, which also yielded therapeutic levels of HP-fVIII in hemophilia A mice. Based on these studies, an optimized vector contains the HP-fVIII transgene driven by a CMV internal promoter within a SIV-based lentiviral backbone lacking a WPRE.

  2. Nitrogen Backbone Oligomers.

    PubMed

    Wang, Hongbo; Eremets, Mikhail I; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-08-19

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35 GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10 GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2 GPa according to the calculations.

  3. Nitrogen Backbone Oligomers

    PubMed Central

    Wang, Hongbo; Eremets, Mikhail I.; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-01-01

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35 GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10 GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2 GPa according to the calculations. PMID:26286836

  4. Fuzzy logic controller optimization

    DOEpatents

    Sepe, Jr., Raymond B; Miller, John Michael

    2004-03-23

    A method is provided for optimizing a rotating induction machine system fuzzy logic controller. The fuzzy logic controller has at least one input and at least one output. Each input accepts a machine system operating parameter. Each output produces at least one machine system control parameter. The fuzzy logic controller generates each output based on at least one input and on fuzzy logic decision parameters. Optimization begins by obtaining a set of data relating each control parameter to at least one operating parameter for each machine operating region. A model is constructed for each machine operating region based on the machine operating region data obtained. The fuzzy logic controller is simulated with at least one created model in a feedback loop from a fuzzy logic output to a fuzzy logic input. Fuzzy logic decision parameters are optimized based on the simulation.

  5. Discrete Variational Optimal Control

    NASA Astrophysics Data System (ADS)

    Jiménez, Fernando; Kobilarov, Marin; Martín de Diego, David

    2013-06-01

    This paper develops numerical methods for optimal control of mechanical systems in the Lagrangian setting. It extends the theory of discrete mechanics to enable the solutions of optimal control problems through the discretization of variational principles. The key point is to solve the optimal control problem as a variational integrator of a specially constructed higher dimensional system. The developed framework applies to systems on tangent bundles, Lie groups, and underactuated and nonholonomic systems with symmetries, and can approximate either smooth or discontinuous control inputs. The resulting methods inherit the preservation properties of variational integrators and result in numerically robust and easily implementable algorithms. Several theoretical examples and a practical one, the control of an underwater vehicle, illustrate the application of the proposed approach.

  6. Cα-C bond cleavage of the peptide backbone in MALDI in-source decay using salicylic acid derivative matrices.

    PubMed

    Asakawa, Daiki; Takayama, Mitsuo

    2011-07-01

    The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H](+). The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H](+) to that of non-oxidized protonated molecule [M + H](+) of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ≒ 2,5-dihydroxyl benzoic acid (2,5-DHB) ≒ 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the Cα-C bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the Cα-C bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.

  7. Structural basis for the enhanced stability of protein model compounds and peptide backbone unit in ammonium ionic liquids.

    PubMed

    Vasantha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama

    2012-10-04

    Protein folding/unfolding is a fascinating study in the presence of cosolvents, which protect/disrupt the native structure of protein, respectively. The structure and stability of proteins and their functional groups may be modulated by the addition of cosolvents. Ionic liquids (ILs) are finding a vast array of applications as novel cosolvents for a wide variety of biochemical processes that include protein folding. Here, the systematic and quantitative apparent transfer free energies (ΔG'(tr)) of protein model compounds from water to ILs through solubility measurements as a function of IL concentration at 25 °C have been exploited to quantify and interpret biomolecular interactions between model compounds of glycine peptides (GPs) with ammonium based ILs. The investigated aqueous systems consist of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), tetraglycine (Gly(4)), and cyclic glycylglycine (c(GG)) in the presence of six ILs such as diethylammonium acetate (DEAA), diethylammonium hydrogen sulfate (DEAS), triethylammonium acetate (TEAA), triethylammonium hydrogen sulfate (TEAS), triethylammonium dihydrogen phosphate (TEAP), and trimethylammonium acetate (TMAA). We have observed positive values of ΔG'(tr) for GPs from water to ILs, indicating that interactions between ILs and GPs are unfavorable, which leads to stabilization of the structure of model protein compounds. Moreover, our experimental data ΔG'(tr) is used to obtain transfer free energies (Δg'(tr)) of the peptide backbone unit (or glycyl unit) (-CH(2)C═ONH-), which is the most numerous group in globular proteins, from water to IL solutions. To obtain the mechanism events of the ILs' role in enhancing the stability of the model compounds, we have further obtained m-values for GPs from solubility limits. These results explicitly elucidate that all alkyl ammonium ILs act as stabilizers for model compounds through the exclusion of ILs from model compounds of

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

    PubMed Central

    2012-01-01

    Background Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening. Results We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better. Conclusions Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. PMID:22536902

  9. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone1[OPEN

    PubMed Central

    Fraga, Patricia

    2017-01-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3. In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1. We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer. PMID:27956490

  10. Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy.

    PubMed

    de Medeiros, Luciano Neves; Angeli, Renata; Sarzedas, Carolina G; Barreto-Bergter, Eliana; Valente, Ana Paula; Kurtenbach, Eleonora; Almeida, Fabio C L

    2010-02-01

    Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH.

  11. Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics.

    PubMed

    López-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, José Ricardo

    2014-06-01

    Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51), R(52), S(53) in loop 3; F(107), D(108), Y(109), W(111), Y(112), W(115) in loop 7; Q(129), Y(132), D(134), M(135), Y(136), Y(137), G(138) in helix-α2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81), A(82), T(83), G(84) in loop 5, and A(85), A(87) in strand-β5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR.

  12. Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations.

    PubMed

    Letellier, R; Ghomi, M; Taillandier, E

    1989-02-01

    A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.

  13. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries

    NASA Astrophysics Data System (ADS)

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-04-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides.Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. Electronic supplementary information (ESI) available: Experimental details, BET, SEM, XPS and more electrochemical data. See DOI: 10.1039/c5nr01015b

  14. Uranyl mediated photofootprinting reveals strong E. coli RNA polymerase--DNA backbone contacts in the +10 region of the DeoP1 promoter open complex.

    PubMed Central

    Jeppesen, C; Nielsen, P E

    1989-01-01

    Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex. The results show strong polymerase DNA backbone contacts in the -40, -10, and most notably in the +10 region. These results suggest that unwinding of the -12 to +3 region of the promoter in the open complex is mediated through polymerase DNA backbone contacts on both sides of this region. The pattern of bases that are hyperreactive towards KMnO4 or uranyl within the -12 to +3 region furthermore argues against a model in which this region is simply unwound and/or single stranded. The results indicate specific protein contacts and/or a fixed DNA conformation within the -12 to +3 region. Images PMID:2503811

  15. Study of a chimeric foot-and-mouth disease virus DNA vaccine containing structural genes of serotype O in a genome backbone of serotype Asia 1 in guinea pigs.

    PubMed

    Chockalingam, A K; Thiyagarajan, S; Govindasamy, N; Patnaikuni, R; Garlapati, S; Golla, R R; Joyappa, D H; Krishnamshetty, P; Veluvarti, V V S; Veluvati, V V S

    2010-01-01

    Since foot-and-mouth disease virus (FMDV) serotypes display a great genetic and antigenic diversity, there is a constant requirement to monitor the performance of FMDV vaccines in the field with respect to their antigenic coverage. To avoid possible antigenic changes in field FMDV isolates during their adaptation to BHK-21 cells, a standard step used in production of conventional FMDV vaccines, the custom-made chimeric conventional or DNA vaccines, in which antigenic determinants are replaced with those of appropriate field strains, should be constructed. Using this approach, we made a plasmid-based chimeric FMDV DNA vaccine containing structural genes of serotype O in the genome backbone of serotype Asia 1, all under the control of Human cytomegalovirus (HCMV) immediate early gene promoter. BHK-21 cells transfected with the chimeric DNA vaccine did not show cytopathic effect (CPE), but expressed virus-specific proteins as demonstrated by 35S-methionine labeling and immunoprecipitation. Guinea pigs immunized with the chimeric DNA vaccine produced virus-specific antibodies assayed by ELISA and virus neutralization test (VNT), respectively. The chimeric DNA vaccine showed a partial protection of guinea pigs challenged with the virulent FMDV. Although the chimeric DNA vaccine, in general, was not as effective as a conventional one, this study encourages further work towards the development of genetically engineered custom-made chimeric vaccines against FMDV.

  16. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries.

    PubMed

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-05-07

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides.

  17. Small Angle Neutron Scattering Study of Conformation of Oligo(ethylene glycol) Grafted Polystyrene in Dilute Solutions: Effect of the Backbone Length

    SciTech Connect

    Cheng, Gang; Hong, Kunlun; Hua, Fengjun; Melnichenko, Yuri B; Wignall, George D; Mays, Jimmy

    2008-01-01

    The conformation and clusterization of comb like polymers of polystyrene densely grafted with oligo(ethylene glycol) (OEG) side chains in 1.0 wt% solutions of D2O, toluene-d8 and methanol-d4 was investigated as a function of the degree of polymerization (DP) of the backbone by small angle neutron scattering (SANS). Each side chain had four EG repeat units and the DP of the polystyrene backbone was varied from 8 to 85. The global conformation of the polymers in toluene and methanol was shown to assume ellipsoidal, cylindrical or worm-like chain morphologies with increasing DP of the polystyrene backbone. At the same time, in D2O, the polymer conformation was described by the form factor of rigid cylinders. The second viral coefficient was measured for the polymer with a DP of 85 in all three solvents and the solvent quality of toluene, methanol and D2O was identified as good, marginal and poor for this polymer. Due to a poor solvent quality, the PS backbone (DP = 85) is partially collapsed in D2O whereas it is moderately expanded in toluene and methanol. Polymers with the DP of 8 were found to aggregate into clusters in all three solvents, with the characteristic size between 100 and 200 ?and a fractal dimension of 2. With increase of the DP, the clusters diminished in D2O and completely disappeared in toluene and methanol. This observation suggests that the clusterization of these short side-chain polymers is caused by end group and hydrogen bonding interactions between different chains.

  18. A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

    PubMed Central

    Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

    2014-01-01

    α-Synuclein is an intrinsically disordered protein of 140 residues that switches to an α-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential HN–Hα and HN–HN NOEs, values for 3JHNHα, 1JHαCα, 2JCαN, and 1JCαN, as well as chemical shifts of 15N, 13Cα, and 13C′ nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20–30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone β region (20–40%) than seen in the database. A generally lower population of the αR region (10–20%) is found. Analysis of 1H–1H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein. PMID:24976112

  19. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  20. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

    PubMed

    Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

    2002-01-01

    Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

  1. Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group.

    PubMed

    Rhee, Hanju; Lee, Jang-Soo; Lee, Jihae; Joo, Cheonik; Han, Hogyu; Cho, Minhaeng

    2008-02-21

    Alanine dipeptide analog 1 backbone-caged with a photolabile linker, 4,5-dimethoxy-2-nitrobenzyl (DmNb), was synthesized. UV-pulse-induced photochemical reaction of 1 was monitored by Fourier transform IR absorption spectroscopy under a steady-state condition or in a fast-scan mode. Upon photolysis of 1, the amide I band is changed from a doublet to a singlet with concomitant line shape changes of several IR bands. The change of the amide I band is directly associated with the photocleavage of the covalent N-C bond connecting the backbone amide of 2 to DmNb. Therefore, IR spectroscopy is useful for directly probing the photocleavage of backbone-caged peptide 1 and the concurrent release of native peptide 2. In contrast, UV-vis spectroscopy probing the irradiation-induced structural change of the 2-nitrobenzyl moiety itself may not provide a clue directly relevant to the photocleavage of such N-C bond. Time-resolved IR spectra recorded in a fast-scan mode after pulsed UV irradiation of 1 reveal that such photocleavage occurs at least faster than a few seconds of our instrumental time resolution.

  2. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose

    PubMed Central

    Yi, Gang-Shun; Wang, Wei-Wei; Cao, Wei-Guo; Wang, Feng-Ping; Liu, Xi-Peng

    2017-01-01

    Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes. PMID:28106786

  3. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose.

    PubMed

    Yi, Gang-Shun; Wang, Wei-Wei; Cao, Wei-Guo; Wang, Feng-Ping; Liu, Xi-Peng

    2017-01-18

    Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2' hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2'-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs' catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.

  4. In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone

    SciTech Connect

    Baxa, U.; Wall, J.; Keller, P. W.; Cheng, N.; Steven, A. C.

    2011-01-01

    In yeast cells infected with the [PSI+] prion, Sup35p forms aggregates and its activity in translation termination is downregulated. Transfection experiments have shown that Sup35p filaments assembled in vitro are infectious, suggesting that they reproduce or closely resemble the prion. We have used several EM techniques to study the molecular architecture of filaments, seeking clues as to the mechanism of downregulation. Sup35p has an N-terminal 'prion' domain; a highly charged middle (M-)domain; and a C-terminal domain with the translation termination activity. By negative staining, cryo-EM and scanning transmission EM (STEM), filaments of full-length Sup35p show a thin backbone fibril surrounded by a diffuse 65-nm-wide cloud of globular C-domains. In diameter ({approx}8 nm) and appearance, the backbones resemble amyloid fibrils of N-domains alone. STEM mass-per-unit-length data yield -1 subunit per 0.47 nm for N-fibrils, NM-filaments and Sup35p filaments, further supporting the fibril backbone model. The 30 nm radial span of decorating C-domains indicates that the M-domains assume highly extended conformations, offering an explanation for the residual Sup35p activity in infected cells, whereby the C-domains remain free enough to interact with ribosomes.

  5. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86% of optimal.

    PubMed

    Hart, W E; Istrail, S

    1997-01-01

    This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. We consider two side chain models: a lattice model that generalizes the HP model (Dill, 1985) to explicitly represent side chains on the cubic lattice and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. We describe algorithms with mathematically guaranteed error bounds for both of these models. In particular, we describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 86% of optimal in a face-centered cubic lattice, and we demonstrate how this provides a better than 70% performance guarantee for the HP-TSSC model. Our analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Ngo et al. (1994) concerning the complexity of protein folding models that include side chains.

  6. Numerical Optimization Using Computer Experiments

    NASA Technical Reports Server (NTRS)

    Trosset, Michael W.; Torczon, Virginia

    1997-01-01

    Engineering design optimization often gives rise to problems in which expensive objective functions are minimized by derivative-free methods. We propose a method for solving such problems that synthesizes ideas from the numerical optimization and computer experiment literatures. Our approach relies on kriging known function values to construct a sequence of surrogate models of the objective function that are used to guide a grid search for a minimizer. Results from numerical experiments on a standard test problem are presented.

  7. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  8. Utility of Climate Forecasts in promoting optimal inter-basin transfer in the North Carolina Triangle Area Weihua Li, Sankarasubramanian Arumugam and Ranji S. Ranjithan Department of Civil, Construction and Environmental Engineering North Carolina State University

    NASA Astrophysics Data System (ADS)

    Li, W.; Arumugam, S.; Ranjithan, R.

    2011-12-01

    Droughts experienced by regional water supply systems often result due to reduced streamflow/precipitation potential which could occur due to varying exogenous climatic conditions such as tropical sea surface temperature (SST). Similarly, water supply systems can also experience frequent shortages in supply due to increased water demand resulting from urbanization and population growth in the region. The goal of this study is to identify a sustainable way of managing triangle area's two major reservoir systems while in the meantime improving the water supply reliability for its urban area. In this study, the water resource availability within this area is determined using a predefined water surplus index, which indicates an uneven distribution of the available water resource. Therefore, combined with streamflow forecasts downscaled from GCM climate forecasts for the summer season, an integrated reservoir simulation-optimization model is developed to explore the potential benefit of inter-basin transfer between Falls Lake of the Neuse River basin and Jordan Lake in the Cape Fear River basin. Using the 3-month ahead ensembles of streamflow forecasts, the reservoir simulation model can estimate the average end of season storage deviation from the target storage across the two systems under the predefined inter-basin transfer scenario. Then the optimization model helps identify the optimal transfers among the systems that can minimize the average end of season storage deviation, while in the mean time sustain the water demand for the area. Results of the analysis for the period 1991~2008 show that by introducing inter-basin transfer, the reliability of the water supply systems for the triangle area could be increased, which would help in developing regional drought management strategies. Key words: Drought, climate forecast, inter-basin transfer

  9. Generalized Newton-Raphson trajectory optimization-generator 1

    NASA Technical Reports Server (NTRS)

    Cope, D. D.; Eskridge, C. D.; Hanafy, L. M.

    1968-01-01

    Computer program constructs a sequence of optimal solutions to dynamically-approximate linear equations. Specification of the number and type of subarcs in the optimal solution allows simultaneous satisfaction of all switching criteria.

  10. Two Egyptian Construction Tools.

    ERIC Educational Resources Information Center

    Lamb, John F., Jr.

    1993-01-01

    Describes the geometric concepts involved in two construction tools used in ancient Egypt. A level is used to make a construction horizontal, and the plumb level is used to make a construction vertical. (MDH)

  11. Beuchler Construction Information Sheet

    EPA Pesticide Factsheets

    Beuchler Construction (the Company) is located in Bismarck, North Dakota. The settlement involves renovation activities conducted at a property constructed prior to 1978, located in Bismarck, North Dakota.

  12. Stonke Construction Information Sheet

    EPA Pesticide Factsheets

    Stonke Construction (the Company) is located in Anchorage, Alaska. The settlement involves renovation activities conducted at properties constructed prior to 1978, located in and around Anchorage, Alaska.

  13. Distributed Optimization

    NASA Technical Reports Server (NTRS)

    Macready, William; Wolpert, David

    2005-01-01

    We demonstrate a new framework for analyzing and controlling distributed systems, by solving constrained optimization problems with an algorithm based on that framework. The framework is ar. information-theoretic extension of conventional full-rationality game theory to allow bounded rational agents. The associated optimization algorithm is a game in which agents control the variables of the optimization problem. They do this by jointly minimizing a Lagrangian of (the probability distribution of) their joint state. The updating of the Lagrange parameters in that Lagrangian is a form of automated annealing, one that focuses the multi-agent system on the optimal pure strategy. We present computer experiments for the k-sat constraint satisfaction problem and for unconstrained minimization of NK functions.

  14. Advanced construction management for lunar base construction - Surface operations planner

    NASA Technical Reports Server (NTRS)

    Kehoe, Robert P.

    1992-01-01

    The study proposes a conceptual solution and lays the framework for developing a new, sophisticated and intelligent tool for a lunar base construction crew to use. This concept integrates expert systems for critical decision making, virtual reality for training, logistics and laydown optimization, automated productivity measurements, and an advanced scheduling tool to form a unique new planning tool. The concept features extensive use of computers and expert systems software to support the actual work, while allowing the crew to control the project from the lunar surface. Consideration is given to a logistics data base, laydown area management, flexible critical progress scheduler, video simulation of assembly tasks, and assembly information and tracking documentation.

  15. Prospective Optimization.

    PubMed

    Sejnowski, Terrence J; Poizner, Howard; Lynch, Gary; Gepshtein, Sergei; Greenspan, Ralph J

    2014-05-01

    Human performance approaches that of an ideal observer and optimal actor in some perceptual and motor tasks. These optimal abilities depend on the capacity of the cerebral cortex to store an immense amount of information and to flexibly make rapid decisions. However, behavior only approaches these limits after a long period of learning while the cerebral cortex interacts with the basal ganglia, an ancient part of the vertebrate brain that is responsible for learning sequences of actions directed toward achieving goals. Progress has been made in understanding the algorithms used by the brain during reinforcement learning, which is an online approximation of dynamic programming. Humans also make plans that depend on past experience by simulating different scenarios, which is called prospective optimization. The same brain structures in the cortex and basal ganglia that are active online during optimal behavior are also active offline during prospective optimization. The emergence of general principles and algorithms for goal-directed behavior has consequences for the development of autonomous devices in engineering applications.

  16. Prospective Optimization

    PubMed Central

    Sejnowski, Terrence J.; Poizner, Howard; Lynch, Gary; Gepshtein, Sergei; Greenspan, Ralph J.

    2014-01-01

    Human performance approaches that of an ideal observer and optimal actor in some perceptual and motor tasks. These optimal abilities depend on the capacity of the cerebral cortex to store an immense amount of information and to flexibly make rapid decisions. However, behavior only approaches these limits after a long period of learning while the cerebral cortex interacts with the basal ganglia, an ancient part of the vertebrate brain that is responsible for learning sequences of actions directed toward achieving goals. Progress has been made in understanding the algorithms used by the brain during reinforcement learning, which is an online approximation of dynamic programming. Humans also make plans that depend on past experience by simulating different scenarios, which is called prospective optimization. The same brain structures in the cortex and basal ganglia that are active online during optimal behavior are also active offline during prospective optimization. The emergence of general principles and algorithms for goal-directed behavior has consequences for the development of autonomous devices in engineering applications. PMID:25328167

  17. Construction progress of the RHIC electron lenses

    SciTech Connect

    Fischer W.; Altinbas, Z.; Anerella, M.; Beebe, E.; et al

    2012-05-20

    In polarized proton operation the RHIC performance is limited by the head-on beam-beam effect. To overcome this limitation two electron lenses are under construction. We give an overview of the construction progress. Guns, collectors and the warm electron beam transport solenoids with their power supplies have been constructed. The superconducting solenoids that guide the electron beam during the interaction with the proton beam are near completion. A test stand has been set up to verify the performance of the gun, collector and some of the instrumentation. The infrastructure is being prepared for installation, and simulations continue to optimize the performance.

  18. Space construction data base

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Construction of large systems in space is a technology requiring the development of construction methods to deploy, assemble, and fabricate the elements comprising such systems. A construction method is comprised of all essential functions and operations and related support equipment necessary to accomplish a specific construction task in a particular way. The data base objective is to provide to the designers of large space systems a compendium of the various space construction methods which could have application to their projects.

  19. Synthesis of long-circulating, backbone degradable HPMA copolymer-doxorubicin conjugates and evaluation of molecular-weight-dependent antitumor efficacy.

    PubMed

    Pan, Huaizhong; Sima, Monika; Yang, Jiyuan; Kopeček, Jindřich

    2013-02-01

    Backbone degradable, linear, multiblock N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-doxorubicin (DOX) conjugates are synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization followed by chain extension via thiol-ene click reaction. The examination of molecular-weight-dependent antitumor activity toward human ovarian A2780/AD carcinoma in nude mice reveals enhanced activity of multiblock, second-generation, higher molecular weight conjugates when compared with traditional HPMA copolymer-DOX conjugates. The examination of body weight changes during treatment indicates the absence of non-specific adverse effects.

  20. Backbone assignments of the 26 kDa neuron-specific ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1).

    PubMed

    Andersson, Fredrik I; Jackson, Sophie E; Hsu, Shang-Te Danny

    2010-04-01

    UCH-L1 is a member of the family of ubiquitin C-terminal hydrolases whose primary role is to hydrolyze small C-terminal adducts of ubiquitin to generate free ubiquitin monomers. Expression of UCH-L1 is highly specific to neurons and point mutations in this enzyme are associated with a hereditary form of Parkinson's disease. Herein, we present the NMR backbone assignments of human UCH-L1, thus enabling future solution-state NMR spectroscopic studies on the structure and function of this important protein.