Replacement of charged and polar residues in the coiled-coiled interface of huntingtin-interacting protein 1 (HIP1) causes aggregation and cell death.

PubMed

Fontaine, Sarah N; Bauer, Scott P; Lin, Xiaoyan; Poorfarahani, Sara; Ybe, Joel A

2012-09-21

HIP1 crystal structures solved in our laboratory revealed abnormalities in the coiled-coil region, suggesting intrinsic plasticity. To test this, specific amino acids in the coiled-coil were mutated. The apparent thermal stability of HIP1 was altered when Thr528 and Glu531 were replaced by leucine, and was enhanced when Lys510 was also mutated. In cells, HIP1 mutant expression produced aggregation. MTS and flow cytometry indicate a correlation between aggregated HIP1 and enhanced cell death. These data support the idea that flexibility of the HIP1 coiled-coil domain is important for normal function and may lead to new insights into Huntington's disease. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Rotatable superconducting cyclotron adapted for medical use

DOEpatents

Blosser, Henry G.; Johnson, David A.; Riedel, Jack; Burleigh, Richard J.

1985-01-01

A superconducting cyclotron (10) rotatable on a support structure (11) in an arc of about 180.degree. around a pivot axis (A--A) and particularly adapted for medical use is described. The rotatable support structure (13, 15) is balanced by being counterweighted (14) so as to allow rotation of the cyclotron and a beam (12), such as a subparticle (neutron) or atomic particle beam, from the cyclotron in the arc around a patient. Flexible hose (25) is moveably attached to the support structure for providing a liquified gas which is supercooled to near 0.degree. K. to an inlet means (122) to a chamber (105) around superconducting coils (101, 102). The liquid (34) level in the cyclotron is maintained approximately half full so that rotation of the support structure and cyclotron through the 180.degree. can be accomplished without spilling the liquid from the cyclotron. With the coils vertically oriented, each turn of the winding is approximately half immersed in liquid (34) and half exposed to cold gas and adequate cooling to maintain superconducting temperatures in the section of coil above the liquid level is provided by the combination of cold gas/vapor and by the conductive flow of heat along each turn of the winding from the half above the liquid to the half below.

All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

NASA Astrophysics Data System (ADS)

Woo, Sun Young; Lee, Hwankyu

2016-03-01

Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

PubMed

Woo, Sun Young; Lee, Hwankyu

2016-03-01

Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

Manufacture and Quality Control of Insert Coil with Real ITER TF Conductor

DOE PAGES

Ozeki, H.; Isono, T.; Uno, Y.; ...

2016-03-02

JAEA successfully completed the manufacture of the toroidal field (TF) insert coil (TFIC) for a performance test of the ITER TF conductor in the final design in cooperation with Hitachi, Ltd. The TFIC is a single-layer 8.875-turn solenoid coil with 1.44-m diameter. This will be tested for 68-kA current application in a 13-T external magnetic field. TFIC was manufactured in the following order: winding of the TF conductor, lead bending, fabrication of the electrical termination, heat treatment, turn insulation, installation of the coil into the support mandrel structure, vacuum pressure impregnation (VPI), structure assembly, and instrumentation. Here in this presentation,more » manufacture process and quality control status for the TFIC manufacturing are reported.« less

Crystal structure at 2.8 A of the DLLRKN-containing coiled-coil domain of huntingtin-interacting protein 1 (HIP1) reveals a surface suitable for clathrin light chain binding.

PubMed

Ybe, Joel A; Mishra, Sanjay; Helms, Stephen; Nix, Jay

2007-03-16

Huntingtin interacting protein 1 (HIP1) is a member of a family of proteins whose interaction with Huntingtin is critical to prevent cells from initiating apoptosis. HIP1, and related protein HIP12/1R, can also bind to clathrin and membrane phospholipids, and HIP12/1R links the CCV to the actin cytoskeleton. HIP1 and HIP12/1R interact with the clathrin light chain EED regulatory site and stimulate clathrin lattice assembly. Here, we report the X-ray structure of the coiled-coil domain of HIP1 (residues 482-586) that includes residues crucial for binding clathrin light chain. The dimeric HIP1 crystal structure is partially splayed open. The comparison of the HIP1 model with coiled-coil predictions revealed the heptad repeat in the dimeric trunk (S2 path) is offset relative to the register of the heptad repeat from the N-terminal portion (S1 path) of the molecule. Furthermore, surface analysis showed there is a third hydrophobic path (S3) running parallel with S1 and S2. We present structural evidence supporting a role for the S3 path as an interaction surface for clathrin light chain. Finally, comparative analysis suggests the mode of binding between sla2p and clathrin light chain may be different in yeast.

MAST magnetic diagnostics

NASA Astrophysics Data System (ADS)

Edlington, T.; Martin, R.; Pinfold, T.

2001-01-01

The mega-ampere spherical tokamak (MAST) experiment is a new, large, low aspect ratio device (R=0.7-0.8 m, a=0.5-0.65 m, maximum BT˜0.63 T at R=0.7 m) operating its first experimental physics campaign. Designed to study a wide variety of plasma shapes with up to 2 MA of plasma current with an aspect ratio down to 1.3, the poloidal field (PF) coils used for plasma formation, equilibrium and shaping are inside the main vacuum vessel. For plasma control and to investigate a wide range of plasma phenomena, an extensive set of magnetic diagnostics have been installed inside the vacuum vessel. More than 600 vacuum compatible, bakeable diagnostic coils are configured in a number of discrete arrays close to the plasma edge with about half the coils installed behind the graphite armour tiles covering the center column. The coil arrays measure the toroidal and poloidal variation in the equilibrium field and its high frequency fluctuating components. Internal coils also measure currents in the PF coils, plasma current, stored energy and induced currents in the mechanical support structures of the coils and graphite armour tiles. The latter measurements are particularly important when halo currents are induced following a plasma termination, for example, when the plasma becomes vertically unstable. The article describes the MAST magnetic diagnostic coil set and their calibration. The way in which coil signals are used to control the plasma equilibrium is described and data from the first MAST experimental campaign presented. These coil data are used as input to the code EFIT [L. Lao et al., Nucl. Fusion 25, 1611 (1985)], for measurement of halo currents in the vacuum vessel structure and for measurements of the structure of magnetic field fluctuations near the plasma edge.

A pulsed eddy current probe for inspection of support plates from within Alloy-800 steam generator tubes

NASA Astrophysics Data System (ADS)

Krause, T. W.; Babbar, V. K.; Underhill, P. R.

2014-02-01

Support plate degradation and fouling in nuclear steam generators (SGs) can lead to SG tube corrosion and loss of efficiency. Inspection and monitoring of these conditions can be integrated with preventive maintenance programs, thereby advancing station-life management processes. A prototype pulsed eddy current (PEC) probe, targeting inspection issues associated with SG tubes in SS410 tube support plate structures, has been developed using commercial finite element (FE) software. FE modeling was used to identify appropriate driver and pickup coil configurations for optimum sensitivity to changes in gap and offset for Alloy-800 SG tubes passing through 25 mm thick SS410 support plates. Experimental measurements using a probe that was manufactured based on the modeled configuration, were used to confirm the sensitivity of differential PEC signals to changes in relative position of the tube within the tube support plate holes. Models investigated the effect of shift and tilt of tube with respect to hole centers. Near hole centers and for small shifts, modeled signal amplitudes from the differentially connected coil pairs were observed to change linearly with tube shift. This was in agreement with experimentally measured TEC coil response. The work paves the way for development of a system targeting the inspection and evaluation of support plate structures in steam generators.

Fail-Safe Magnetic Bearing Controller Demonstrated Successfully

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.; Provenza, Andrew J.

2001-01-01

The Structural Mechanics and Dynamics Branch has successfully demonstrated a fail-safe controller for the Fault-Tolerant Magnetic Bearing rig at the NASA Glenn Research Center. The rotor is supported by two 8-pole redundant radial bearings, and coil failing situations are simulated by manually shutting down their control current commands from the controller cockpit. The effectiveness of the controller was demonstrated when only two active coils from each radial bearing could be used (that is, 14 coils failed). These remaining two coils still levitated the rotor and spun it without losing stability or desired position up to the maximum allowable speed of 20,000 rpm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozeki, H.; Isono, T.; Uno, Y.

JAEA successfully completed the manufacture of the toroidal field (TF) insert coil (TFIC) for a performance test of the ITER TF conductor in the final design in cooperation with Hitachi, Ltd. The TFIC is a single-layer 8.875-turn solenoid coil with 1.44-m diameter. This will be tested for 68-kA current application in a 13-T external magnetic field. TFIC was manufactured in the following order: winding of the TF conductor, lead bending, fabrication of the electrical termination, heat treatment, turn insulation, installation of the coil into the support mandrel structure, vacuum pressure impregnation (VPI), structure assembly, and instrumentation. Here in this presentation,more » manufacture process and quality control status for the TFIC manufacturing are reported.« less

Cross-linking reveals laminin coiled-coil architecture

PubMed Central

Armony, Gad; Jacob, Etai; Moran, Toot; Levin, Yishai; Mehlman, Tevie; Levy, Yaakov; Fass, Deborah

2016-01-01

Laminin, an ∼800-kDa heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. The unique architecture of laminin is not currently amenable to determination at high resolution, as its flexible and narrow segments complicate both crystallization and single-particle reconstruction by electron microscopy. Therefore, we used cross-linking and MS, evaluated using computational methods, to address key questions regarding laminin quaternary structure. This approach was particularly well suited to the ∼750-Å coiled coil that mediates trimer assembly, and our results support revision of the subunit order typically presented in laminin schematics. Furthermore, information on the subunit register in the coiled coil and cross-links to downstream domains provide insights into the self-assembly required for interaction with other extracellular matrix and cell surface proteins. PMID:27815530

Large-scale synthesis of coiled-like shaped carbon nanotubes using bi-metal catalyst

NASA Astrophysics Data System (ADS)

Krishna, Vemula Mohana; Somanathan, T.; Manikandan, E.; Umar, Ahmad; Maaza, M.

2018-02-01

Carbon nanomaterials (CNMs), especially carbon nanotubes (CNTs) with coiled structure exhibit scientifically fascinating. They may be projected as an innovative preference to future technological materials. Coiled carbon nanotubes (c-CNTs) on a large-scale were successfully synthesized with the help of bi-metal substituted α-alumina nanoparticles catalyst via chemical vapor deposition (CVD) technique. Highly spring-like carbon nanostructures were observed by field emission scanning electron microscope (FESEM) examination. Furthermore, the obtained material has high purity, which correlates the X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectroscopy (EDX) analysis. Raman spectroscopy reveals that the carbon multi layers are well graphitized and crystalline, even if they have defects in its structure due to coiled morphology. High-resolution transmission electron microscope (HRTEM) describes internal structure and dia of the product. Ultimately, results support the activity of bi-metal impregnated α-alumina nanoparticles catalyst to determine the high yield, graphitization and internal structure of the material. We have also studied the purified c-CNTs magnetic properties at room temperature and will be an added advantage in several applications.

Crystal structure at 2.8 Å of the DLLRKN-containing coiled-coil domain of Huntingtin-interacting protein 1 (HIP1) reveals a surface suitable for clathrin light chain binding

PubMed Central

Ybe, Joel A.; Mishra, Sanjay; Helms, Stephen; Nix, Jay

2007-01-01

Summary Huntingtin interacting protein 1 (HIP1) is a member of a family of proteins whose interaction with Huntingtin is critical to prevent cells from initiating apoptosis. HIP1, and related protein HIP12/1R, can also bind to clathrin and membrane phospholipids and HIP12/1R links the CCV to the actin cytoskeleton. HIP1 and HIP12/1R interact with the clathrin light chain EED regulatory site and stimulate clathrin lattice assembly. Here we report the X-ray structure of the coiled-coil domain of HIP1 from 482–586 that includes residues crucial for binding clathrin light chain. The dimeric HIP1 crystal structure is partially splayed open. The comparison of the HIP1 model with coiled-coil predictions revealed the heptad repeat in the dimeric trunk (S2 path) is offset relative to the register of the heptad repeat from the N-terminal portion (S1 path) of the molecule. Furthermore, surface analysis showed there is a third hydrophobic path (S3) running parallel to S1 and S2. We present structural evidence supporting a role for S3 path as an interaction surface for clathrin light chain. Finally, comparative analysis suggests the mode of binding between sla2p and clathrin light chain may be different in yeast. PMID:17257618

Conceptual design and thermal analysis of a modular cryostat for one single coil of a 10 MW offshore superconducting wind turbine

NASA Astrophysics Data System (ADS)

Sun, Jiuce; Sanz, Santiago; Neumann, Holger

2015-12-01

Superconducting generators show the potential to reduce the head mass of large offshore wind turbines. A 10 MW offshore superconducting wind turbine has been investigated in the SUPRAPOWER project. The superconducting coils based on MgB2 tapes are supposed to work at cryogenic temperature of 20 K. In this paper, a novel modular rotating cryostat was presented for one single coil of the superconducting wind turbine. The modular concept and cryogen-free cooling method were proposed to fulfil the requirements of handling, maintenance, reliability of long term and offshore operations. Two stage Gifford-McMahon cryocoolers were used to provide cooling source. Supporting rods made of titanium alloy were selected as support structures of the cryostat in aim of reducing the heat load. The thermal performance in the modular cryostat was carefully investigated. The heat load applied to the cryocooler second stage was 2.17 W@20 K per coil. The corresponding temperature difference along the superconducting coil was only around 1 K.

A new twist in the coil: functions of the coiled-coil domain of structural maintenance of chromosome (SMC) proteins.

PubMed

Matityahu, Avi; Onn, Itay

2018-02-01

The higher-order organization of chromosomes ensures their stability and functionality. However, the molecular mechanism by which higher order structure is established is poorly understood. Dissecting the activity of the relevant proteins provides information essential for achieving a comprehensive understanding of chromosome structure. Proteins of the structural maintenance of chromosome (SMC) family of ATPases are the core of evolutionary conserved complexes. SMC complexes are involved in regulating genome dynamics and in maintaining genome stability. The structure of all SMC proteins resembles an elongated rod that contains a central coiled-coil domain, a common protein structural motif in which two α-helices twist together. In recent years, the imperative role of the coiled-coil domain to SMC protein activity and regulation has become evident. Here, we discuss recent advances in the function of the SMC coiled coils. We describe the structure of the coiled-coil domain of SMC proteins, modifications and interactions that are mediated by it. Furthermore, we assess the role of the coiled-coil domain in conformational switches of SMC proteins, and in determining the architecture of the SMC dimer. Finally, we review the interplay between mutations in the coiled-coil domain and human disorders. We suggest that distinctive properties of coiled coils of different SMC proteins contribute to their distinct functions. The discussion clarifies the mechanisms underlying the activity of SMC proteins, and advocates future studies to elucidate the function of the SMC coiled coil domain.

A periodic table of coiled-coil protein structures.

PubMed

Moutevelis, Efrosini; Woolfson, Derek N

2009-01-23

Coiled coils are protein structure domains with two or more alpha-helices packed together via interlacing of side chains known as knob-into-hole packing. We analysed and classified a large set of coiled-coil structures using a combination of automated and manual methods. This led to a systematic classification that we termed a "periodic table of coiled coils," which we have made available at http://coiledcoils.chm.bris.ac.uk/ccplus/search/periodic_table. In this table, coiled-coil assemblies are arranged in columns with increasing numbers of alpha-helices and in rows of increased complexity. The table provides a framework for understanding possibilities in and limits on coiled-coil structures and a basis for future prediction, engineering and design studies.

Low temperature superconductor and aligned high temperature superconductor magnetic dipole system and method for producing high magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Ramesh; Scanlan, Ronald; Ghosh, Arup K.

A dipole-magnet system and method for producing high-magnetic-fields, including an open-region located in a radially-central-region to allow particle-beam transport and other uses, low-temperature-superconducting-coils comprised of low-temperature-superconducting-wire located in radially-outward-regions to generate high magnetic-fields, high-temperature-superconducting-coils comprised of high-temperature-superconducting-tape located in radially-inward-regions to generate even higher magnetic-fields and to reduce erroneous fields, support-structures to support the coils against large Lorentz-forces, a liquid-helium-system to cool the coils, and electrical-contacts to allow electric-current into and out of the coils. The high-temperature-superconducting-tape may be comprised of bismuth-strontium-calcium-copper-oxide or rare-earth-metal, barium-copper-oxide (ReBCO) where the rare-earth-metal may be yttrium, samarium, neodymium, or gadolinium. Advantageously, alignment of themore » large-dimension of the rectangular-cross-section or curved-cross-section of the high-temperature-superconducting-tape with the high-magnetic-field minimizes unwanted erroneous magnetic fields. Alignment may be accomplished by proper positioning, tilting the high-temperature-superconducting-coils, forming the high-temperature-superconducting-coils into a curved-cross-section, placing nonconducting wedge-shaped-material between windings, placing nonconducting curved-and-wedge-shaped-material between windings, or by a combination of these techniques.« less

Applying graph theory to protein structures: an atlas of coiled coils.

PubMed

Heal, Jack W; Bartlett, Gail J; Wood, Christopher W; Thomson, Andrew R; Woolfson, Derek N

2018-05-02

To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterised experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analysing this resource. Here, we use tools from graph theory to define an atlas classification scheme for automatically categorising certain protein substructures. Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein-protein interaction motifs, we present a suite of computational resources designed for analysing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the 'dark matter' of coiled-coil structures; i.e., those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design. iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.

Predicting helix orientation for coiled-coil dimers

PubMed Central

Apgar, James R.; Gutwin, Karl N.; Keating, Amy E.

2008-01-01

The alpha-helical coiled coil is a structurally simple protein oligomerization or interaction motif consisting of two or more alpha helices twisted into a supercoiled bundle. Coiled coils can differ in their stoichiometry, helix orientation and axial alignment. Because of the near degeneracy of many of these variants, coiled coils pose a challenge to fold recognition methods for structure prediction. Whereas distinctions between some protein folds can be discriminated on the basis of hydrophobic/polar patterning or secondary structure propensities, the sequence differences that encode important details of coiled-coil structure can be subtle. This is emblematic of a larger problem in the field of protein structure and interaction prediction: that of establishing specificity between closely similar structures. We tested the behavior of different computational models on the problem of recognizing the correct orientation - parallel vs. antiparallel - of pairs of alpha helices that can form a dimeric coiled coil. For each of 131 examples of known structure, we constructed a large number of both parallel and antiparallel structural models and used these to asses the ability of five energy functions to recognize the correct fold. We also developed and tested three sequenced-based approaches that make use of varying degrees of implicit structural information. The best structural methods performed similarly to the best sequence methods, correctly categorizing ∼81% of dimers. Steric compatibility with the fold was important for some coiled coils we investigated. For many examples, the correct orientation was determined by smaller energy differences between parallel and antiparallel structures distributed over many residues and energy components. Prediction methods that used structure but incorporated varying approximations and assumptions showed quite different behaviors when used to investigate energetic contributions to orientation preference. Sequence based methods were sensitive to the choice of residue-pair interactions scored. PMID:18506779

Osmolyte effects on helix formation in peptides and the stability of coiled-coils

PubMed Central

Celinski, Scott A.; Scholtz, J. Martin

2002-01-01

The ability of several naturally occurring substances known as osmolytes to induce helix formation in an alanine-based peptide have been investigated. As predicted by the osmophobic effect hypothesis, the osmolytes studies here do induce helix formation. Trimethylamine-N-oxide (TMAO) is the best structure-inducing osmolytes investigated here, but it is not as effective in promoting helix formation as the common cosolvent trifluoroethanol (TFE). We also provide a semiquantitative study of the ability of TMAO to induce helix formation and urea, which acts as a helix (and protein) denaturant. We find that on a molar basis, these agents are exactly counteractive as structure inducing and unfolding agents. Finally, we extend the investigations to the effects of urea and TMAO on the stability of a dimeric coiled-coil peptide and find identical results. Together these results support the tenets of the osmophobic hypothesis and highlight the importance of the polypeptide backbone in protein folding and stability. PMID:12142459

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peter H. Titus and Ali Zolfaghari

A critical design feature of any tokamak is the space taken up by the inner leg of the toroidal field (TF) coil. The radial build needed for the TF inner leg, along with shield thickness , size of the central solenoid and plasma minor radius set the major radius of the machine. The cost of the tokamak core roughly scales with the cube of the major radius. Small reductions in the TF build can have a big impact on the overall cost of the reactor. The cross section of the TF inner leg must structurally support the centering force andmore » that portion of the vertical separating force that is not supported by the outer structures. In this paper, the TF inner leg equatorial plane cross sections are considered. Out-of- Plane (OOP) forces must also be supported, but these are largest away from the equatorial plane, in the inner upper and lower corners and outboard sections of the TF coil. OOP forces are taken by structures that are not closely coupled with the radial build of the central column at the equatorial plane. The "Vertical Access AT Pilot Plant" currently under consideration at PPPL is used as a starting point for the structural, field and current requirements. Other TF structural concepts are considered. Most are drawn from existing designs such as ITER's circular conduits in radial plates bearing on a heavy nose section, and TPX's square conduits in a case, Each of these concepts can rely on full wedging, or partial wedging. Vaulted TF coils are considered as are those with some component of bucking against a central solenoid or bucking post. With the expectation that the pilot plant will be a steady state machine, a static stress criteria is used for all the concepts. The coils are assumed to be superconducting, with the superconductor not contributing to the structural strength. Limit analysis is employed to assess the degree of conservatism in the static criteria as it is applied to a linear elastic stress analysis. TF concepts, and in particular the PPPL AT PILOT plate concept are evaluated based on amount of space needed for structure and the amount of space left for superconductor.« less

Quantitative analysis of the radiation error for aerial coiled-fiber-optic distributed temperature sensing deployments using reinforcing fabric as support structure

NASA Astrophysics Data System (ADS)

Sigmund, Armin; Pfister, Lena; Sayde, Chadi; Thomas, Christoph K.

2017-06-01

In recent years, the spatial resolution of fiber-optic distributed temperature sensing (DTS) has been enhanced in various studies by helically coiling the fiber around a support structure. While solid polyvinyl chloride tubes are an appropriate support structure under water, they can produce considerable errors in aerial deployments due to the radiative heating or cooling. We used meshed reinforcing fabric as a novel support structure to measure high-resolution vertical temperature profiles with a height of several meters above a meadow and within and above a small lake. This study aimed at quantifying the radiation error for the coiled DTS system and the contribution caused by the novel support structure via heat conduction. A quantitative and comprehensive energy balance model is proposed and tested, which includes the shortwave radiative, longwave radiative, convective, and conductive heat transfers and allows for modeling fiber temperatures as well as quantifying the radiation error. The sensitivity of the energy balance model to the conduction error caused by the reinforcing fabric is discussed in terms of its albedo, emissivity, and thermal conductivity. Modeled radiation errors amounted to -1.0 and 1.3 K at 2 m height but ranged up to 2.8 K for very high incoming shortwave radiation (1000 J s-1 m-2) and very weak winds (0.1 m s-1). After correcting for the radiation error by means of the presented energy balance, the root mean square error between DTS and reference air temperatures from an aspirated resistance thermometer or an ultrasonic anemometer was 0.42 and 0.26 K above the meadow and the lake, respectively. Conduction between reinforcing fabric and fiber cable had a small effect on fiber temperatures (< 0.18 K). Only for locations where the plastic rings that supported the reinforcing fabric touched the fiber-optic cable were significant temperature artifacts of up to 2.5 K observed. Overall, the reinforcing fabric offers several advantages over conventional support structures published to date in the literature as it minimizes both radiation and conduction errors.

Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils.

PubMed

Groth, Mike C; Rink, W Mathis; Meyer, Nils F; Thomas, Franziska

2018-05-14

Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants ( K D ) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-A x B y and the newly characterized C-A x B y . Both comprise K D values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a competitive binding model, giving rate constants and overall affinities of the underlying association and dissociation reactions. The overall affinities correlate well with the ratios of K D values determined by CD-thermal denaturation experiments and, hence, support the dissociative mechanism of strand displacement in heterodimeric coiled coils. From the results of more than 100 different displacement reactions we are able to classify three categories of overall affinities, which allow for easy prediction of the equilibrium of strand displacement in two competing heterodimeric coiled coils.

Long-Lived Pure Electron Plasma in Ring Trap-1

NASA Astrophysics Data System (ADS)

Saitoh, Haruhiko; Yoshida, Zensho; Morikawa, Junji; Watanabe, Sho; Yano, Yoshihisa; Suzuki, Junko

The Ring Trap-1 (RT-1) experiment succeeded in producing a long-lived (of the order 102 s), stable, non-neutral (pure electron) plasma. Electrons are confined by a magnetospheric dipole field. To eliminate a loss channel of the plasmas caused by support structures, a superconducting coil was magnetically levitated. This coil levitation drastically improved the confinement properties of the electron plasma compared to previous Prototype-Ring Trap (Proto-RT) experiments.

Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05342h

PubMed Central

Groth, Mike C.; Rink, W. Mathis; Meyer, Nils F.

2018-01-01

Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants (KD) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-AxBy and the newly characterized C-AxBy. Both comprise KD values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a competitive binding model, giving rate constants and overall affinities of the underlying association and dissociation reactions. The overall affinities correlate well with the ratios of KD values determined by CD-thermal denaturation experiments and, hence, support the dissociative mechanism of strand displacement in heterodimeric coiled coils. From the results of more than 100 different displacement reactions we are able to classify three categories of overall affinities, which allow for easy prediction of the equilibrium of strand displacement in two competing heterodimeric coiled coils. PMID:29780562

Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

PubMed

Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

2015-06-01

The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. © 2015 Wiley Periodicals, Inc.

Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain.

PubMed

Tao, Y; Strelkov, S V; Mesyanzhinov, V V; Rossmann, M G

1997-06-15

Oligomeric coiled-coil motifs are found in numerous protein structures; among them is fibritin, a structural protein of bacteriophage T4, which belongs to a class of chaperones that catalyze a specific phage-assembly process. Fibritin promotes the assembly of the long tail fibers and their subsequent attachment to the tail baseplate; it is also a sensing device that controls the retraction of the long tail fibers in adverse environments and, thus, prevents infection. The structure of fibritin had been predicted from sequence and biochemical analyses to be mainly a triple-helical coiled coil. The determination of its structure at atomic resolution was expected to give insights into the assembly process and biological function of fibritin, and the properties of modified coiled-coil structures in general. The three-dimensional structure of fibritin E, a deletion mutant of wild-type fibritin, was determined to 2.2 A resolution by X-ray crystallography. Three identical subunits of 119 amino acid residues form a trimeric parallel coiled-coil domain and a small globular C-terminal domain about a crystallographic threefold axis. The coiled-coil domain is divided into three segments that are separated by insertion loops. The C-terminal domain, which consists of 30 residues from each subunit, contains a beta-propeller-like structure with a hydrophobic interior. The residues within the C-terminal domain make extensive hydrophobic and some polar intersubunit interactions. This is consistent with the C-terminal domain being important for the correct assembly of fibritin, as shown earlier by mutational studies. Tight interactions between the C-terminal residues of adjacent subunits counteract the latent instability that is suggested by the structural properties of the coiled-coil segments. Trimerization is likely to begin with the formation of the C-terminal domain which subsequently initiates the assembly of the coiled coil. The interplay between the stabilizing effect of the C-terminal domain and the labile coiled-coil domain may be essential for the fibritin function and for the correct functioning of many other alpha-fibrous proteins.

Crystal Structure of a Coiled-Coil Domain from Human ROCK I

PubMed Central

Tu, Daqi; Li, Yiqun; Song, Hyun Kyu; Toms, Angela V.; Gould, Christopher J.; Ficarro, Scott B.; Marto, Jarrod A.; Goode, Bruce L.; Eck, Michael J.

2011-01-01

The small GTPase Rho and one of its targets, Rho-associated kinase (ROCK), participate in a variety of actin-based cellular processes including smooth muscle contraction, cell migration, and stress fiber formation. The ROCK protein consists of an N-terminal kinase domain, a central coiled-coil domain containing a Rho binding site, and a C-terminal pleckstrin homology domain. Here we present the crystal structure of a large section of the central coiled-coil domain of human ROCK I (amino acids 535–700). The structure forms a parallel α-helical coiled-coil dimer that is structurally similar to tropomyosin, an actin filament binding protein. There is an unusual discontinuity in the coiled-coil; three charged residues (E613, R617 and D620) are positioned at what is normally the hydrophobic core of coiled-coil packing. We speculate that this conserved irregularity could function as a hinge that allows ROCK to adopt its autoinhibited conformation. PMID:21445309

The C-terminal coiled-coil of the bacterial voltage-gated sodium channel NaChBac is not essential for tetramer formation, but stabilizes subunit-to-subunit interactions.

PubMed

Mio, Kazuhiro; Mio, Muneyo; Arisaka, Fumio; Sato, Masahiko; Sato, Chikara

2010-09-01

The NaChBac is a prokaryotic homologue of the voltage-gated sodium channel found in the genome of the alkalophilic bacterium Bacillus halodurans C-125. Like a repeating cassette of mammalian sodium channel, the NaChBac possesses hydrophobic domains corresponding to six putative transmembrane segments and a pore loop, and exerts channel function by forming a tetramer although detailed mechanisms of subunit assembly remain unclear. We generated truncated mutants from NaChBac, and investigated their ability to form tetramers in relation to their channel functions. A mutant that deletes almost all of the C-terminal coiled-coil structure lost its voltage-dependent ion permeability, although it was properly translocated to the cell surface. The mutant protein was purified as a tetramer using a reduced concentration of detergent, but the association between the subunits was shown to be much weaker than the wild type. The chemical cross-linking, blue native PAGE, sedimentation velocity experiments, size exclusion chromatography, immunoprecipitation, and electron microscopy all supported its tetrameric assembly. We further purified the C-terminal cytoplasmic domain alone and confirmed its self-oligomerization. These data suggest that the C-terminal coiled-coil structure stabilizes subunit-to-subunit interactions of NaChBac, but is not critical for their tetramer formation. 2010 Elsevier Ltd. All rights reserved.

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.

PubMed

Wood, Christopher W; Bruning, Marc; Ibarra, Amaurys Á; Bartlett, Gail J; Thomson, Andrew R; Sessions, Richard B; Brady, R Leo; Woolfson, Derek N

2014-11-01

The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/. © The Author 2014. Published by Oxford University Press.

Magnetic-field sensing coil embedded in ceramic for measuring ambient magnetic field

DOEpatents

Takahashi, Hironori

2004-02-10

A magnetic pick-up coil for measuring magnetic field with high specific sensitivity, optionally with an electrostatic shield (24), having coupling elements (22) with high winding packing ratio, oriented in multiple directions, and embedded in ceramic material for structural support and electrical insulation. Elements of the coil are constructed from green ceramic sheets (200) and metallic ink deposited on surfaces and in via holes of the ceramic sheets. The ceramic sheets and the metallic ink are co-fired to create a monolithic hard ceramic body (20) with metallized traces embedded in, and placed on exterior surfaces of, the hard ceramic body. The compact and rugged coil can be used in a variety of environments, including hostile conditions involving ultra-high vacuum, high temperatures, nuclear and optical radiation, chemical reactions, and physically demanding surroundings, occurring either individually or in combinations.

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain.

PubMed

Wilbur, Jeremy D; Hwang, Peter K; Brodsky, Frances M; Fletterick, Robert J

2010-03-01

Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.

A new type of coil structure called pan-shaped coil of wireless charging system based on magnetic resonance

NASA Astrophysics Data System (ADS)

Yue, Z. K.; Liu, Z. Z.; Hou, Y. J.; Zeng, H.; Liang, L. H.; Cui, S.

2017-11-01

The problem that misalignment between the transmitting coil and the receiving coil significantly impairs the transmission power and efficiency of the system has been attached more and more attention. In order to improve the uniformity of the magnetic field between the two coils to solve this problem, a new type of coil called pan-shaped coil is proposed. Three-dimension simulation models of the planar-core coil and the pan-shaped coil are established using Ansoft Maxwell software. The coupling coefficient between the transmitting coil and the receiving coil is obtained by simulating the magnetic field with the receiving coil misalignment or not. And the maximum percentage difference strength along the radial direction which is defined as the magnetic field uniformity factor is calculated. According to the simulation results of the two kinds of coil structures, it is found that the new type of coil structure can obviously improve the uniformity of the magnetic field, coupling coefficient and power transmission properties between the transmitting coil and the receiving coil.

High-Temperature Superconductors as Electromagnetic Deployment and Support Structures in Spacecraft. [NASA NIAC Phase I

NASA Technical Reports Server (NTRS)

Getliffe, Gwendolyn V.; Inamdar, Niraj K.; Masterson, Rebecca; Miller, David W.

2012-01-01

This report, concluding a one-year NIAC Phase I study, describes a new structural and mechanical technique aimed at reducing the mass and increasing the deployed-to-stowed length and volume ratios of spacecraft systems. This technique uses the magnetic fields generated by electrical current passing through coils of high-temperature superconductors (HTSs) to support spacecraft structures and deploy them to operational configurations from their stowed positions inside a launch vehicle fairing.

Computational assessment of folding energy landscapes in heterodimeric coiled coils.

PubMed

André, Ingemar; Bjelic, Sinisa

2018-07-01

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes. © 2018 Wiley Periodicals, Inc.

Performance of the Conduction-Cooled LDX Levitation Coil

NASA Astrophysics Data System (ADS)

Michael, P. C.; Schultz, J. H.; Smith, B. A.; Titus, P. H.; Radovinsky, A.; Zhukovsky, A.; Hwang, K. P.; Naumovich, G. J.; Camille, R. J.

2004-06-01

The Levitated Dipole Experiment (LDX) was developed to study plasma confinement in a dipole magnetic field. Plasma is confined in the magnetic field of a 680-kg Nb3Sn Floating Coil (F-coil) that is electromagnetically supported at the center of a 5-m diameter by 3-m tall vacuum chamber. The Levitation Coil (L-coil) is a 2800-turn, double pancake winding that supports the weight of the F-coil and controls its vertical position within the vacuum chamber. The use of high-temperature superconductor (HTS) Bi-2223 for the L-coil minimizes the electrical and cooling power needed for levitation. The L-coil winding pack and support plate are suspended within the L-coil cryostat and cooled by conduction to a single-stage cryocooler rated for 25-W heat load at approximately 20 K. The coil current leads consist of conduction-cooled copper running from room temperature to 80 K and a pair of commercially-available, 150-A HTS leads. An automatically filled liquid-nitrogen reservoir provides cooling for the coil's radiation shield and for the leads' 80-K heat stations. This paper discusses the L-coil system design and its observed cryogenic performance.

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caillat, Christophe; Fish, Alexander; Pefani, Dafni-Eleftheria

The GemC1 coiled-coil structure has subtle differences compared with its homologues Geminin and Idas. Co-expression experiments in cells and biophysical stability analysis of the Geminin-family coiled coils suggest that the GemC1 coiled coil alone is unstable. GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. GemC1 shows a less typical coiled coil compared with the Geminin homodimer and themore » Geminin–Idas heterodimer structures. It is also shown that both in vitro and in cells GemC1 interacts with Geminin through its coiled-coil domain, forming a heterodimer that is more stable that the GemC1 homodimer. Comparative analysis of the thermal stability of all of the possible superfamily complexes, using circular dichroism to follow the unfolding of the entire helix of the coiled coil, or intrinsic tryptophan fluorescence of a unique conserved N-terminal tryptophan, shows that the unfolding of the coiled coil is likely to take place from the C-terminus towards the N-terminus. It is also shown that homodimers show a single-state unfolding, while heterodimers show a two-state unfolding, suggesting that the dimer first falls apart and the helices then unfold according to the stability of each protein. The findings argue that Geminin-family members form homodimers and heterodimers between them, and this ability is likely to be important for modulating their function in cycling and differentiating cells.« less

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilbur, Jeremy D., E-mail: jwilbur@msg.ucsf.edu; Hwang, Peter K.; Brodsky, Frances M.

2010-03-01

Variable packing interaction related to the conformational flexibility within the huntingtin-interacting protein 1 coiled coil domain. Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington’s disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coilmore » domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.« less

Multi-Canted Coils, Tubes, and Structures

NASA Technical Reports Server (NTRS)

Jaster, Mark L. (Inventor)

2015-01-01

Coil, tube, and other structures configured with a plurality of individual coils, internal structures, legs or extensions with each having multiple cants per coil, internal structure, leg or extension, and wherein the cants formed therein allow for a load-deflection force when each is compressed. In addition, any horizontal or moment forces are substantially reduced and/or eliminated when a downward vertical force is applied, as minimal or no torsion is created in the individual coils, legs or extensions.

Structural deformation upon protein-protein interaction: A structural alphabet approach

PubMed Central

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-01-01

Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking. PMID:18307769

Structural deformation upon protein-protein interaction: a structural alphabet approach.

PubMed

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-02-28

In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

Automated de novo phasing and model building of coiled-coil proteins.

PubMed

Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

2015-03-01

Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure.

PubMed

Parry, David A D; Fraser, R D Bruce; Squire, John M

2008-09-01

alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

Crystal Structure of the Central Coiled-Coil Domain from Human Liprin-[beta]2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stafford, Ryan L.; Tang, Ming-Yun; Sawaya, Michael R.

2012-02-07

Liprins are a conserved family of scaffolding proteins important for the proper regulation and development of neuronal synapses. Humans have four liprin-{alpha}s and two liprin-{beta}s which all contain long coiled-coil domains followed by three tandem SAM domains. Complex interactions between the coiled-coil and SAM domains are thought to create liprin scaffolds, but the structural and biochemical properties of these domains remain largely uncharacterized. In this study we find that the human liprin-{beta}2 coiled-coil forms an extended dimer. Several protease-resistant subdomains within the liprin-{beta}1 and liprin-{beta}2 coiled-coils were also identified. A 2.0 {angstrom} crystal structure of the central, protease-resistant core ofmore » the liprin-{beta}2 coiled-coil reveals a parallel helix orientation. These studies represent an initial step toward determining the overall architecture of liprin scaffolds and understanding the molecular basis for their synaptic functions.« less

TPX: Contractor preliminary design review. Volume 3, Design and analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-06-30

Several models have been formed for investigating the maximum electromagnetic loading and magnetic field levels associated with the Tokamak Physics eXperiment (TPX) superconducting Poloidal Field (PF) coils. The analyses have been performed to support the design of the individual fourteen hoop coils forming the PF system. The coils have been sub-divided into three coil systems consisting of the central solenoid (CS), PF5 coils, and the larger radius PF6 and PF7 coils. Various electromagnetic analyses have been performed to determine the electromagnetic loadings that the coils will experience during normal operating conditions, plasma disruptions, and fault conditions. The loadings are presentedmore » as net body forces acting individual coils, spatial variations throughout the coil cross section, and force variations along the path of the conductor due to interactions with the TF coils. Three refined electromagnetic models of the PF coil system that include a turn-by-turn description of the fields and forces during a worst case event are presented in this report. A global model including both the TF and PF system was formed to obtain the force variations along the path of the PF conductors resulting from interactions with the TF currents. In addition to spatial variations, the loadings are further subdivided into time-varying and steady components so that structural fatigue issues can be addressed by designers and analysts. Other electromagnetic design issues such as the impact of the detailed coil designs on field errors are addressed in this report. Coil features that are analyzed include radial transitions via short jogs vs. spiral type windings and the effects of layer-to-layer rotations (i.e clocking) on the field errors.« less

2-d and 1-d Nanomaterials Construction through Peptide Computational Design and Solution Assembly

NASA Astrophysics Data System (ADS)

Pochan, Darrin

Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic/H-bonding/hydrophobic interactions to define hierarchical material structure and consequent properties. Importantly, while biomimicry has been a successful strategy for the design of new peptide molecules for intermolecular assembly, computational tools have been developed to de novo design peptide molecules required for construction of pre-determined, desired nanostructures and materials. A new system comprised of coiled coil bundle motifs theoretically designed to assemble into designed, one and two-dimensional nanostructures will be introduced. The strategy provides the opportunity for arbitrary nanostructure formation, i.e. structures not observed in nature, with peptide molecules. Importantly, the desired nanostructure was chosen first while the peptides needed for coiled coil formation and subsequent nanomaterial formation were determined computationally. Different interbundle, two-dimensional nanostructures are stabilized by differences in amino acid composition exposed on the exterior of the coiled coil bundles. Computation was able to determine molecules required for different interbundle symmetries within two-dimensional sheets stabilized by subtle differences in amino acid composition of the inherent peptides. Finally, polymers were also created through covalent interactions between bundles that allowed formation of architectures spanning flexible network forming chains to ultra-stiff polymers, all with the same building block peptides. The success of the computational design strategy is manifested in the nanomaterial results as characterized by electron microscopy, scattering methods, and biophysical techniques. Support from NSF DMREF program under awards DMR-1234161 and DMR-1235084.

Parametric design studies of toroidal magnetic energy storage units

NASA Astrophysics Data System (ADS)

Herring, J. Stephen

Superconducting magnetic energy storage (SMES) units have a number of advantages as storage devices. Electrical current is the input, output and stored medium, allowing for completely solid-state energy conversion. The magnets themselves have no moving parts. The round trip efficiency is higher than those for batteries, compressed air or pumped hydro. Output power can be very high, allowing complete discharge of the unit within a few seconds. Finally, the unit can be designed for a very large number of cycles, limited basically by fatigue in the structural components. A small systems code was written to produce and evaluate self-consistent designs for toroidal superconducting energy storage units. The units can use either low temperature or high temperature superconductors. The coils have D shape where the conductor and its stabilizer/structure is loaded only in tension and the centering forces are borne by a bucking cylinder. The coils are convectively cooled from a cryogenic reservoir in the bore of the coils. The coils are suspended in a cylindrical metal shell which protects the magnet during rail, automotive or shipboard use. It is important to note that the storage unit does not rely on its surroundings for structural support, other than normal gravity and inertial loads. Designs are presented for toroidal energy storage units produced by the systems code. A wide range of several parameters have been considered, resulting in units storing from 1 MJ to 72 GJ. Maximum fields range from 5 T to 20 T. The masses and volumes of the coils, bucking cylinder, coolant, insulation and outer shell are calculated. For unattended use, the allowable operating time using only the boiloff of the cryogenic fluid for refrigeration is calculated. For larger units, the coils were divided into modules suitable for normal truck or rail transport.

New tetrameric forms of the rotavirus NSP4 with antiparallel helices.

PubMed

Kumar, Sushant; Ramappa, Raghavendra; Pamidimukkala, Kiranmayee; Rao, C D; Suguna, K

2018-06-01

Rotavirus nonstructural protein 4, the first viral enterotoxin to be identified, is a multidomain, multifunctional glycoprotein. Earlier, we reported a Ca 2+ -bound coiled-coil tetrameric structure of the diarrhea-inducing region of NSP4 from the rotavirus strains SA11 and I321 and a Ca 2+ -free pentameric structure from the rotavirus strain ST3, all with a parallel arrangement of α-helices. pH was found to determine the oligomeric state: a basic pH favoured a tetramer, whereas an acidic pH favoured a pentamer. Here, we report two novel forms of the coiled-coil region of NSP4 from the bovine rotavirus strains MF66 and NCDV. These crystallized at acidic pH, forming antiparallel coiled-coil tetrameric structures without any bound Ca 2+ ion. Structural and mutational studies of the coiled-coil regions of NSP4 revealed that the nature of the residue at position 131 (Tyr/His) plays an important role in the observed structural diversity.

Larp Nb3Sn Quadrupole Magnets for the Lhc Luminosity Upgrade

NASA Astrophysics Data System (ADS)

Ferracin, P.

2010-04-01

The US LHC Accelerator Research Program (LARP) is a collaboration between four US laboratories (BNL, FNAL, LBNL, and SLAC) aimed at contributing to the commissioning and operation of the LHC and conducting R&D on its luminosity upgrade. Within LARP, the Magnet Program's main goal is to demonstrate that Nb3Sn superconducting magnets are a viable option for a future upgrade of the LHC Interaction Regions. Over the past four years, LARP has successfully fabricated and tested several R&D magnets: 1) the subscale quadrupole magnet SQ, to perform technology studies with 300 mm long racetrack coils, 2) the technology quadrupole TQ, to investigate support structure behavior with 1 m long cos 2θ coils, and 3) the long racetrack magnet LR, to test 3.6 m long racetrack coils. The next milestone consists in the fabrication and test of the 3.7 m long quadrupole magnet LQ, with the goal of demonstrating that Nb3Sn technology is mature for use in high energy accelerators. After an overview of design features and test result of the LARP magnets fabricated so far, this paper focuses on the status of the fabrication of LQ: we describe the production of the 3.4 m long cos 2θ coils, and the of the qualification support structure. Finally, the status of the development of the next 1 m long model HQ, conceived to explore stress and field limits of Nb3Sn superconducting, magnets, is presented.

High Radiation Environment Nuclear Fragment Separator Magnet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kahn, Stephen; Gupta, Ramesh

2016-01-31

Superconducting coils wound with HTS conductor can be used in magnets located in a high radiation environment. NbTi and Nb 3Sn superconductors must operate at 4.5 K or below where removal of heat is less efficient. The HTS conductor can carry significant current at higher temperatures where the Carnot efficiency is significantly more favorable and where the coolant heat capacity is much larger. Using the HTS conductor the magnet can be operated at 40 K. This project examines the use of HTS conductor for the Michigan State University Facility For Rare Isotope Beams (FRIB) fragment separator dipole magnet which bendsmore » the beam by 30° and is located in a high radiation region that will not be easily accessible. Two of these magnets are needed to select the chosen isotope. There are a number of technical challenges to be addressed in the design of this magnet. The separator dipole is 2 m long and subtends a large angle. The magnet should keep a constant transverse field profile along its beam reference path. Winding coils with a curved inner segment is difficult as the conductor will tend to unwind during the process. In the Phase I project two approaches to winding the conductor were examined. The first was to wind the coils with curved sections on the inner and outer segments with the inner segment wound with negative curvature. The alternate approach was to use a straight segment on the inner segment to avoid negative curvature. In Phase I coils with a limited number of turns were successfully wound and tested at 77 K for both coil configurations. The Phase II program concentrated on the design, coil winding procedures, structural analysis, prototyping and testing of an HTS curved dipole coil at 40 K with a heat load representative of the radiation environment. One of the key criteria of the design of this magnet is to avoid the use of organic materials that would degrade rapidly in radiation. The Lorentz forces expected from the coils interacting with the magnetic field are large and in order minimize the deformation of the coils, mechanical support must be provided. Since the support structure cannot be made of organic materials with minimal thermal conductivity, an optimization was explored comparing the amount of coil deformation that can be tolerated and the amount of heat leakage that can be endured. A test coil containing 500 m of HTS was constructed to be tested at the 40 K operating temperature. The anticipated heat load was simulated with heater strips to demonstrate that the heat could be removed and that the coil can operate in a stable state. The FRIB project has decided that using HTS coils for this magnet was too risky considering their time and funding constraints and has opted for a more conservative approach with conventional coils. As an outcome of this STTR project, it is likely that HTS coils operating at higher temperatures will have beneficial applications for future accelerator projects.« less

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

Mechanical Design of HD2, a 15 T Nb3Sn Dipole Magnet with a 35 mm Bore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferracin, P.; Bartlett, S.E.; Caspi, S.

2006-06-01

After the fabrication and test of HD1, a 16 T Nb{sub 3}Sn dipole magnet based on flat racetrack coil configuration, the Superconducting Magnet Program at Lawrence Berkeley National Laboratory (LBNL) is developing the Nb{sub 3}Sn dipole HD2. With a dipole field above 15 T, a 35 mm clear bore, and nominal field harmonics within a fraction of one unit, HD2 represents a further step towards the application of block-type coils to high-field accelerator magnets. The design features tilted racetrack-type ends, to avoid obstructing the beam path, and a 4 mm thick stainless steel tube, to support the coil during themore » preloading operation. The mechanical structure, similar to the one used for HD1, is based on an external aluminum shell pretensioned with pressurized bladders. Axial rods and stainless steel plates provide longitudinal support to the coil ends during magnet excitation. A 3D finite element analysis has been performed to evaluate stresses and deformations from assembly to excitation, with particular emphasis on conductor displacements due to Lorentz forces. Numerical results are presented and discussed.« less

The Molecular Structure of Human Red Blood Cell Membranes from Highly Oriented, Solid Supported Multi-Lamellar Membranes

PubMed Central

Himbert, Sebastian; Alsop, Richard J.; Rose, Markus; Hertz, Laura; Dhaliwal, Alexander; Moran-Mirabal, Jose M.; Verschoor, Chris P.; Bowdish, Dawn M. E.; Kaestner, Lars; Wagner, Christian; Rheinstädter, Maikel C.

2017-01-01

We prepared highly oriented, multi-lamellar stacks of human red blood cell (RBC) membranes applied on silicon wafers. RBC ghosts were prepared by hemolysis and applied onto functionalized silicon chips and annealed into multi-lamellar RBC membranes. High resolution X-ray diffraction was used to determine the molecular structure of the stacked membranes. We present direct experimental evidence that these RBC membranes consist of nanometer sized domains of integral coiled-coil peptides, as well as liquid ordered (lo) and liquid disordered (ld) lipids. Lamellar spacings, membrane and hydration water layer thicknesses, areas per lipid tail and domain sizes were determined. The common drug aspirin was added to the RBC membranes and found to interact with RBC membranes and preferably partition in the head group region of the lo domain leading to a fluidification of the membranes, i.e., a thinning of the bilayers and an increase in lipid tail spacing. Our results further support current models of RBC membranes as patchy structures and provide unprecedented structural details of the molecular organization in the different domains. PMID:28045119

The Molecular Structure of Human Red Blood Cell Membranes from Highly Oriented, Solid Supported Multi-Lamellar Membranes

NASA Astrophysics Data System (ADS)

Himbert, Sebastian; Alsop, Richard J.; Rose, Markus; Hertz, Laura; Dhaliwal, Alexander; Moran-Mirabal, Jose M.; Verschoor, Chris P.; Bowdish, Dawn M. E.; Kaestner, Lars; Wagner, Christian; Rheinstädter, Maikel C.

2017-01-01

We prepared highly oriented, multi-lamellar stacks of human red blood cell (RBC) membranes applied on silicon wafers. RBC ghosts were prepared by hemolysis and applied onto functionalized silicon chips and annealed into multi-lamellar RBC membranes. High resolution X-ray diffraction was used to determine the molecular structure of the stacked membranes. We present direct experimental evidence that these RBC membranes consist of nanometer sized domains of integral coiled-coil peptides, as well as liquid ordered (lo) and liquid disordered (ld) lipids. Lamellar spacings, membrane and hydration water layer thicknesses, areas per lipid tail and domain sizes were determined. The common drug aspirin was added to the RBC membranes and found to interact with RBC membranes and preferably partition in the head group region of the lo domain leading to a fluidification of the membranes, i.e., a thinning of the bilayers and an increase in lipid tail spacing. Our results further support current models of RBC membranes as patchy structures and provide unprecedented structural details of the molecular organization in the different domains.

Coiled-coil destabilizing residues in the group A Streptococcus M1 protein are required for functional interaction.

PubMed

Stewart, Chelsea M; Buffalo, Cosmo Z; Valderrama, J Andrés; Henningham, Anna; Cole, Jason N; Nizet, Victor; Ghosh, Partho

2016-08-23

The sequences of M proteins, the major surface-associated virulence factors of the widespread bacterial pathogen group A Streptococcus, are antigenically variable but have in common a strong propensity to form coiled coils. Paradoxically, these sequences are also replete with coiled-coil destabilizing residues. These features are evident in the irregular coiled-coil structure and thermal instability of M proteins. We present an explanation for this paradox through studies of the B repeats of the medically important M1 protein. The B repeats are required for interaction of M1 with fibrinogen (Fg) and consequent proinflammatory activation. The B repeats sample multiple conformations, including intrinsically disordered, dissociated, as well as two alternate coiled-coil conformations: a Fg-nonbinding register 1 and a Fg-binding register 2. Stabilization of M1 in the Fg-nonbinding register 1 resulted in attenuation of Fg binding as expected, but counterintuitively, so did stabilization in the Fg-binding register 2. Strikingly, these register-stabilized M1 proteins gained the ability to bind Fg when they were destabilized by a chaotrope. These results indicate that M1 stability is antithetical to Fg interaction and that M1 conformational dynamics, as specified by destabilizing residues, are essential for interaction. A "capture-and-collapse" model of association accounts for these observations, in which M1 captures Fg through a dynamic conformation and then collapses into a register 2-coiled coil as a result of stabilization provided by binding energy. Our results support the general conclusion that destabilizing residues are evolutionarily conserved in M proteins to enable functional interactions necessary for pathogenesis.

ETF magnet design alternatives for the national MHD program

NASA Astrophysics Data System (ADS)

Marston, P. G.; Thome, R. J.; Dawson, A. M.; Bobrov, E. S.; Hatch, A. M.

1981-01-01

Five superconducting magnet designs are evaluated for a 200 MWe test facility requiring a magnet with an on-axis field of 6 T, an inlet bore area of 4 sq m, storing 6 x 10 to the 9th J. The designs include a straightforward rectangular saddle coil set, a 'Cask' configuration based on staves and corner blocks as the main support structure, and an internally cooled, cabled superconductor to minimize the substructure and eliminate the helium vessel. Also, a modular design using six coils with individual helium vessels and an integrated structure produces a simplest configuration which utilizes a natural rectangular interface for packaging the MHD channel and its connections, and results in a lower capital cost.

An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.

PubMed

Hirano, Kenji; Yokogawa, Daisuke; Sato, Hirofumi; Sakaki, Shigeyoshi

2010-06-17

Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.

Magnetic Guarding: Experimental and Numerical Results

NASA Astrophysics Data System (ADS)

Heinrich, Jonathon; Font, Gabriel; Garrett, Michael; Rose, D.; Genoni, T.; Welch, D.; McGuire, Thomas

2017-10-01

The magnetic field topology of Lockheed Martin's Compact Fusion Reactor (CFR) concept requires internal magnetic field coils. Internal coils for similar devices have leveraged levitating coils or coils with magnetically guarded supports. Magnetic guarding of supports has been investigated for multipole devices (theoretically and experimentally) without conclusive results. One outstanding question regarding magnetic guarding of supports is the magnitude and behavior of secondary plasma drifts resulting from magnetic guard fields (grad-B drifts, etc). We present magnetic-implicit PIC modeling results and preliminary proof of concept experimental results on magnetic guarding of internal-supports and the subsequent reduction in total plasma losses.

A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations

DOE PAGES

Malashkevich, Vladimir N.; Higgins, Chelsea D.; Almo, Steven C.; ...

2015-05-06

The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here in this paper we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms amore » well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. Finally, these novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.« less

Suppressor Analysis of the Fusogenic Lambda Spanins.

PubMed

Cahill, Jesse; Rajaure, Manoj; Holt, Ashley; Moreland, Russell; O'Leary, Chandler; Kulkarni, Aneesha; Sloan, Jordan; Young, Ry

2017-07-15

The final step of lysis in phage λ infections of Escherichia coli is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of Rz and Rz1 were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants in vivo Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality. IMPORTANCE Caudovirales encode cell envelope-spanning proteins called spanins, which are thought to fuse the inner and outer membranes during phage lysis. Recent genetic analysis identified the functional domains of the lambda spanins, which are similar to class I viral fusion proteins. While the pre- and postfusion structures of model fusion systems have been well characterized, the intermediate structure(s) formed during the fusion reaction remains elusive. Genetic analysis would be expected to identify functional connections between intermediates. Since most membrane fusion systems are not genetically tractable, only few such investigations have been reported. Here, we report a suppressor analysis of lambda spanin function. To our knowledge this is the first suppression analysis of a class I-like complex and also the first such analysis of a prokaryote membrane fusion system. Copyright © 2017 American Society for Microbiology.

Four signature motifs define the first class of structurally related large coiled-coil proteins in plants.

PubMed Central

Gindullis, Frank; Rose, Annkatrin; Patel, Shalaka; Meier, Iris

2002-01-01

Background Animal and yeast proteins containing long coiled-coil domains are involved in attaching other proteins to the large, solid-state components of the cell. One subgroup of long coiled-coil proteins are the nuclear lamins, which are involved in attaching chromatin to the nuclear envelope and have recently been implicated in inherited human diseases. In contrast to other eukaryotes, long coiled-coil proteins have been barely investigated in plants. Results We have searched the completed Arabidopsis genome and have identified a family of structurally related long coiled-coil proteins. Filament-like plant proteins (FPP) were identified by sequence similarity to a tomato cDNA that encodes a coiled-coil protein which interacts with the nuclear envelope-associated protein, MAF1. The FPP family is defined by four novel unique sequence motifs and by two clusters of long coiled-coil domains separated by a non-coiled-coil linker. All family members are expressed in a variety of Arabidopsis tissues. A homolog sharing the structural features was identified in the monocot rice, indicating conservation among angiosperms. Conclusion Except for myosins, this is the first characterization of a family of long coiled-coil proteins in plants. The tomato homolog of the FPP family binds in a yeast two-hybrid assay to a nuclear envelope-associated protein. This might suggest that FPP family members function in nuclear envelope biology. Because the full Arabidopsis genome does not appear to contain genes for lamins, it is of interest to investigate other long coiled-coil proteins, which might functionally replace lamins in the plant kingdom. PMID:11972898

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

PubMed

Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

2017-03-21

To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

A miniature implantable coil that can be wrapped around a tubular organ within the human body

NASA Astrophysics Data System (ADS)

Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

2018-05-01

There are many tubular or rod-shaped organs and tissues within the human body. A miniature medical implant that wraps around such a biological structure can monitor or modulate its function. In order to provide the wrap-around implant with power, a solenoidal coil coupled wirelessly with a planar coil outside the human body can be used. Unfortunately, there is a serious practical problem that this configuration cannot be realized easily because the implantable solenoidal coil cannot be positioned around the tubular biological structure unless either the structure or the coil is cut and reconnected, which is impermissible in most cases. In addition, when a planner exterior coil is used for wireless power transfer and communication, its maximum magnetic coupling with the implanted solenoidal coil is achieved when the tubular structure is perpendicular to the surface of the body. However, in human anatomy, most tubular/rod structures are oriented horizontally. In order to solve these problems, we present a new flexible coil for the class of wrapped-around implantable devices. Our multilayer coil has specially designed windings in cross patterns. The new coil can be made conveniently in high precision at low cost on a flat substrate using the same technology for making the flexible multilayer printed circuit boards along with miniature sensors and electronic circuits. This allows the implant to be made in a flat form and then wrapped around the biostructure during surgery. We present the design of this new coil, perform theoretical analysis with respect to its wireless power transfer efficiency, discuss the effects of coil parameters, and conduct experiments using constructed miniature prototypes. Our results confirm the validity of the new coil.

Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil

PubMed Central

Diao, Jiasheng

2010-01-01

Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 Å resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35° and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35° instead of 18° in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers. PMID:20027625

An innovative design for using flexible printed coils for magnetostrictive-based longitudinal guided wave sensors in steel strand inspection

NASA Astrophysics Data System (ADS)

Tse, P. W.; Liu, X. C.; Liu, Z. H.; Wu, B.; He, C. F.; Wang, X. J.

2011-05-01

Magnetostrictive sensors (MsSs) that can excite and receive guided waves are commonly used in detecting defects that may occur in cables and strands for supporting heavy structures. A conventional MsS has a hard sensing coil that is wound onto a bobbin with electric wires to generate the necessary dynamic magnetic field to excite the desired guided waves. This tailor-made hard coil is usually bulky and is not flexible enough to fit steel strands of various sizes. The conventional MsS also cannot be mounted to any steel strand that does not have a free end to allow the bobbin to pass through the structure of the tested strand. Such inflexibilities limit the use of conventional MsSs in practical situations. To solve these limitations, an innovative type of coil, called a flexible printed coil (FPC), which is made out of flexible printed film, has been designed to replace the inflexible hard coil. The flexible structure of the FPC ensures that the new MsS can be easily installed on and removed from steel strands with different diameters and without free ends. Moreover, the FPC-based MsS can be wrapped into multiple layers due to its thin and flexible design. Although multi-layer FPC creates a minor asymmetry in the dynamic magnetic field, the results of finite element analysis and experiments confirm that the longitudinal guided waves excited by a FPC-based MsS are comparable to those excited by a conventional hard coil MsS. No significant reduction in defect inspection performance was found; in fact, further advantages were identified when using the FPC-based MsS. When acting as the transmitter, the innovative FPC-based MsS can cover a longer inspection length of strand. When acting as the receiver, the FPC-based MsS is more sensitive to smaller defects that are impossible to detect using a hard coil MsS. Hence, the multi-layer FPC-based MsS has great potential for replacing the conventional hard coil MsS because of its convenient installation, and ease of fitting to different strand diameters; it is smaller, and, most importantly, performs much better in strand defect detection.

Biogenesis of the Secretory Granule: Chromogranin a Coiled-Coil Structure Results in Unusual Physical Properties And Suggests a Mechanism for Granule Core Condensation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosley, C.A.; Taupenot, L.; Biswas, N.

2009-06-03

The secretory pro-hormone chromogranin A (CHGA) is densely packed into storage granules along with catecholamines, playing a catalytic role in granule biogenesis. 3-Dimensional structural data on CHGA are lacking. We found a superfamily structural homology for CHGA in the tropomyosin family of alpha-helical coiled-coils, even in mid-molecule regions where primary sequence identity is only modest. The assignment was confirmed by an independent algorithm, suggesting approximately 6-7 such domains spanning CHGA. We provide additional physiochemical evidence (chromatographic, spectral, microscopic) consistent with this unusual structure. Alpha-helical secondary structure (at up to approximately 45%) was confirmed by circular dichroism. CHGA molecular mass wasmore » estimated by MALDI-TOF mass spectrometry at approximately 50 kDa and by denaturing gel filtration at approximately 50-61 kDa, while its native Stokes radius was approximately 84.8 A, as compared to an expected approximately 30 A; the increase gave rise to an apparent native molecular weight of approximately 578 kDa, also consistent with the extended conformation of a coiled-coil. Small-angle X-ray scattering (SAXS) on CHGA in solution best fit an elongated cylindrical conformation in the monodisperse region with a radius of gyration of the rod cross-section (Rt) of approximately 52 A, compatible with a coiled-coil in the hydrated, aqueous state, or a multimeric coiled-coil. Electron microscopy with negative staining revealed an extended, filamentous CHGA structure with a diameter of approximately 94 +/- 4.5 A. Extended, coiled-coil conformation is likely to permit protein 'packing' in the secretory granule at approximately 50% higher density than a globular/spherical conformation. Natural allelic variation in the catestatin region was predicted to disrupt the coiled-coil. Chromaffin granule ultrastructure revealed a approximately 108 +/- 6.3 A periodicity of electron density, suggesting nucleation of a binding complex by the CHGA core. Inhibition of CHGA expression, by siRNA, disrupted regulated secretory protein traffic by approximately 65%, while targeted ablation of the CHGA gene in the mouse reduced chromaffin granule cotransmitter concentrations by approximately 40-80%. These results suggest new roles for secretory protein tertiary structure in hormone and transmitter storage, with implications for secretory cargo condensation (or dense core 'packing' structure) within the regulated pathway.« less

Study on electromagnetic characteristics of the magnetic coupling resonant coil for the wireless power transmission system.

PubMed

Wang, Zhongxian; Liu, Yiping; Wei, Yonggeng; Song, Yilin

2018-01-01

The resonant coil design is taken as the core technology in the magnetic coupling resonant wireless power transmission system, which achieves energy transmission by the coupling of the resonant coil. This paper studies the effect of the resonant coil on energy transmission and the efficiency of the system. Combining a two-coil with a three-coil system, the optimum design method for the resonant coil is given to propose a novel coil structure. First, the co-simulation methods of Pspice and Maxwell are used. When the coupling coefficient of the resonant coil is different, the relationship between system transmission efficiency, output power, and frequency is analyzed. When the self-inductance of the resonant coil is different, the relationship between the performance and frequency of the system transmission is analyzed. Then, two-coil and three-coil structure models are built, and the parameters of the magnetic field of the coils are calculated and analyzed using the finite element method. In the end, a dual E-type simulation circuit model is used to optimize the design of the novel resonance coil. The co-simulation results show that the coupling coefficients of the two-coil, three-coil, and novel coil systems are 0.017, 0.17 and 0.0126, respectively. The power loss of the novel coil is 16.4 mW. There is an obvious improvement in the three-coil system, which shows that the magnetic leakage of the field and the energy coupling are relatively small. The new structure coil has better performance, and the load loss is lower; it can improve the system output power and transmission efficiency.

Shielded helix traveling wave cathode ray tube deflection structure

DOEpatents

Norris, Neil J.; Hudson, Charles L.

1992-01-01

Various embodiments of a helical coil deflection structure of a CRT are described and illustrated which provide shielding between adjacent turns of the coil on either three or four sides of each turn in the coil. Threaded members formed with either male or female threads and having the same pitch as the deflection coil are utilized for shielding the deflection coil with each turn of the helical coil placed between adjacent threads which act to shield each coil turn from adjacent turns and to confine the field generated by the coil to prevent or inhibit cross-coupling between adjacent turns of the coil to thereby prevent generation of fast fields which might otherwise deflect the beam out of time synchronization with the electron beam pulse.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malashkevich, Vladimir N.; Higgins, Chelsea D.; Almo, Steven C.

The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here in this paper we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms amore » well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. Finally, these novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.« less

Coiled Coils - A Model System for the 21st Century.

PubMed

Lupas, Andrei N; Bassler, Jens

2017-02-01

α-Helical coiled coils were described more than 60 years ago as simple, repetitive structures mediating oligomerization and mechanical stability. Over the past 20 years, however, they have emerged as one of the most diverse protein folds in nature, enabling many biological functions beyond mechanical rigidity, such as membrane fusion, signal transduction, and solute transport. Despite this great diversity, their structures can be described by parametric equations, making them uniquely suited for rational protein design. Far from having been exhausted as a source of structural insight and a basis for functional engineering, coiled coils are poised to become even more important for protein science in the coming decades. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal Structure of a Super Leucine Zipper an Extended Two-Stranded Super Long Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Diao

2011-12-31

Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 {angstrom} resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35{sup o} and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through stickymore » hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35{sup o} instead of 18{sup o} in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers.« less

CALUTRONS

DOEpatents

Lawrence, E.O.

1958-09-16

This patent relates to calutron devices and has for its object the arrangement of several independent ion separating mechanisms, i.e., ion source and ion receiver, within a single vacuum tank to econnmize on space and reduce the duplication of magnetic structure. In each of the two described embodiments the ion separating mechanisms are removably supported within the tank. In addition, the magnetic field is produced in the tank by coaxial coils supported outside the tank and magnetic structure is arranged to confine and provide a uniform field within the tank.

Very Fast Current Diagnostic for Linear Pulsed Beams

NASA Astrophysics Data System (ADS)

Nassisi, Vincenzo; Delle Side, Domenico; Turco, Vito

2018-01-01

Fast current pulses manage lasers and particle accelerators and require sophisticate systems to be detected. At today Rogowski coils are well known. They are designed and built with a toroidal structure. In recently application, flat transmission lines are imploded and for this reason we develop a linear Rogowski coil to detect current pulses inside flat conductors. To get deep information from the system, it was approached by means of the theory of the transmission lines. The coil we build presents a resistance but it doesn't influence the rise time of the response, instead the integrating time. We also studied the influence of the magnetic properties of coil support. The new device was able to record pulses of more hundred nanoseconds depending on the inductance, load impedance and resistance of the coil. Furthermore, its response was characterized by a sub-nanosecond rise time ( 100 ps), The attenuation coefficient depends mainly on the turn number of the coil, while the quality of the response depends both on the manufacture quality of the coil and on the magnetic core characteristics. In biophysical applications often, a double line is employed in order to have a sample as control and a sample stressed by a light source. So, in this case we build two equal plane lines by 100 Ω characteristic resistance connected in parallel. We diagnosed the current present in a line. The attenuation factor resulted to be 11,5 A/V.

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

PubMed Central

Lee, Mihwa; Sadowska, Agata; Bekere, Indra; Ho, Diwei; Gully, Benjamin S.; Lu, Yanling; Iyer, K. Swaminathan; Trewhella, Jill; Fox, Archa H.; Bond, Charles S.

2015-01-01

SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism. PMID:25765647

Three-dimensional cell shapes and arrangements in human sweat glands as revealed by whole-mount immunostaining

PubMed Central

Kurata, Ryuichiro; Futaki, Sugiko; Nakano, Itsuko; Fujita, Fumitaka; Tanemura, Atsushi; Murota, Hiroyuki; Katayama, Ichiro; Okada, Fumihiro

2017-01-01

Because sweat secretion is facilitated by mechanical contraction of sweat gland structures, understanding their structure-function relationship could lead to more effective treatments for patients with sweat gland disorders such as heat stroke. Conventional histological studies have shown that sweat glands are three-dimensionally coiled tubular structures consisting of ducts and secretory portions, although their detailed structural anatomy remains unclear. To better understand the details of the three-dimensional (3D) coiled structures of sweat glands, a whole-mount staining method was employed to visualize 3D coiled gland structures with sweat gland markers for ductal luminal, ductal basal, secretory luminal, and myoepithelial cells. Imaging the 3D coiled gland structures demonstrated that the ducts and secretory portions were comprised of distinct tubular structures. Ductal tubules were occasionally bent, while secretory tubules were frequently bent and formed a self-entangled coiled structure. Whole-mount staining of complex coiled gland structures also revealed the detailed 3D cellular arrangements in the individual sweat gland compartments. Ducts were composed of regularly arranged cuboidal shaped cells, while secretory portions were surrounded by myoepithelial cells longitudinally elongated along entangled secretory tubules. Whole-mount staining was also used to visualize the spatial arrangement of blood vessels and nerve fibers, both of which facilitate sweat secretion. The blood vessels ran longitudinally parallel to the sweat gland tubules, while nerve fibers wrapped around secretory tubules, but not ductal tubules. Taken together, whole-mount staining of sweat glands revealed the 3D cell shapes and arrangements of complex coiled gland structures and provides insights into the mechanical contraction of coiled gland structures during sweat secretion. PMID:28636607

Superconducting levitating bearing

NASA Technical Reports Server (NTRS)

Moon, Francis C. (Inventor)

1996-01-01

A superconducting bearing assembly includes a coil field source that may be superconducting and a superconducting structure. The coil field source assembly and superconducting structure are positioned so as to enable relative rotary movement therebetween. The structure and coil field source are brought to a supercooled temperature before a power supply induces a current in the coil field source. A Meissner-like effect is thereby obtained and little or no penetration of the field lines is seen in the superconducting structure. Also, the field that can be obtained from the superconducting coil is 2-8 times higher than that of permanent magnets. Since the magnetic pressure is proportioned to the square of the field, magnetic pressures from 4 to 64 times higher are achieved.

Shielded helix traveling wave cathode ray tube deflection structure

DOEpatents

Norris, N.J.; Hudson, C.L.

1992-12-15

Various embodiments of a helical coil deflection structure of a CRT are described and illustrated which provide shielding between adjacent turns of the coil on either three or four sides of each turn in the coil. Threaded members formed with either male or female threads and having the same pitch as the deflection coil are utilized for shielding the deflection coil with each turn of the helical coil placed between adjacent threads which act to shield each coil turn from adjacent turns and to confine the field generated by the coil to prevent or inhibit cross-coupling between adjacent turns of the coil to thereby prevent generation of fast fields which might otherwise deflect the beam out of time synchronization with the electron beam pulse. 13 figs.

Unraveling double stranded alpha-helical coiled coils: an x-ray diffraction study on hard alpha-keratin fibers.

PubMed

Kreplak, L; Doucet, J; Briki, F

2001-04-15

Transformations of proteins secondary and tertiary structures are generally studied in globular proteins in solution. In fibrous proteins, such as hard alpha-keratin, that contain long and well-defined double stranded alpha-helical coiled coil domains, such study can be directly done on the native fibrous tissue. In order to assess the structural behavior of the coiled coil domains under an axial mechanical stress, wide angle x-ray scattering and small angle x-ray scattering experiments have been carried out on stretched horse hair fibers at relative humidity around 30%. Our observations of the three major axial spacings as a function of the applied macroscopic strain have shown two rates. Up to 4% macroscopic strain the coiled coils were slightly distorted but retained their overall conformation. Above 4% the proportion of coiled coil domains progressively decreased. The main and new result of our study is the observation of the transition from alpha-helical coiled coils to disordered chains instead of the alpha-helical coiled coil to beta-sheet transition that occurs in wet fibers.

Buried polar residues in coiled-coil interfaces.

PubMed

Akey, D L; Malashkevich, V N; Kim, P S

2001-05-29

Coiled coils, estimated to constitute 3-5% of the encoded residues in most genomes, are characterized by a heptad repeat, (abcdefg)(n), where the buried a and d positions form the interface between multiple alpha-helices. Although generally hydrophobic, a substantial fraction ( approximately 20%) of these a- and d-position residues are polar or charged. We constructed variants of the well-characterized coiled coil GCN4-p1 with a single polar residue (Asn, Gln, Ser, or Thr) at either an a or a d position. The stability and oligomeric specificity of each variant were measured, and crystal structures of coiled-coil trimers with threonine or serine at either an a or a d position were determined. The structures show how single polar residues in the interface affect not only local packing, but also overall coiled-coil geometry as seen by changes in the Crick supercoil parameters and core cavity volumes.

Molecular basis of coiled-coil oligomerization-state specificity.

PubMed

Ciani, Barbara; Bjelic, Saša; Honnappa, Srinivas; Jawhari, Hatim; Jaussi, Rolf; Payapilly, Aishwarya; Jowitt, Thomas; Steinmetz, Michel O; Kammerer, Richard A

2010-11-16

Coiled coils are extensively and successfully used nowadays to rationally design multistranded structures for applications, including basic research, biotechnology, nanotechnology, materials science, and medicine. The wide range of applications as well as the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomerization. Here, we address the important and unresolved question why the presence of particular oligomerization-state determinants within a coiled coil does frequently not correlate with its topology. We found an unexpected, general link between coiled-coil oligomerization-state specificity and trigger sequences, elements that are indispensable for coiled-coil formation. By using the archetype coiled-coil domain of the yeast transcriptional activator GCN4 as a model system, we show that well-established trimer-specific oligomerization-state determinants switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence. We successfully confirmed our results in two other, unrelated coiled-coil dimers, ATF1 and cortexillin-1. We furthermore show that multiple topology determinants can coexist in the same trigger sequence, revealing a delicate balance of the resulting oligomerization state by position-dependent forces. Our experimental results should significantly improve the prediction of the oligomerization state of coiled coils. They therefore should have major implications for the rational design of coiled coils and consequently many applications using these popular oligomerization domains.

Test results of the LARP Nb$$_3$$Sn quadrupole HQ03a

DOE PAGES

DiMarco, J.; G. Ambrosio; Chlachidze, G.; ...

2016-03-09

The US LHC Accelerator Research Program (LARP) has been developingmore » $$Nb_3Sn$$ quadrupoles of progressively increasing performance for the high luminosity upgrade of the Large Hadron Collider. The 120 mm aperture High-field Quadrupole (HQ) models are the last step in the R&D phase supporting the development of the new IR Quadrupoles (MQXF). Three series of HQ coils were fabricated and assembled in a shell-based support structure, progressively optimizing the design and fabrication process. The final set of coils consistently applied the optimized design solutions, and was assembled in the HQ03a model. Furthermore, this paper reports a summary of the HQ03a test results, including training, mechanical performance, field quality and quench studies.« less

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

PubMed

Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

PubMed Central

Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

Historical review: another 50th anniversary--new periodicities in coiled coils.

PubMed

Gruber, Markus; Lupas, Andrei N

2003-12-01

In 1953, Francis Crick and Linus Pauling both proposed models of supercoiled alpha helices ('coiled coils') for the structure of keratin. These were the first attempts at modelling the tertiary structure of a protein. Crick emphasized the packing mode of the side-chains ('knobs-into-holes'), which required a periodicity of seven residues over two helical turns (7/2) and a supercoil in the opposite sense of the constituent helices. By contrast, Pauling envisaged a broader set of periodicities (4/1, 7/2, 18/5, 15/4, 11/3) and supercoils of both senses. Crick's model became canonical and the 'heptad repeat' essentially synonymous with coiled coils, but 50 years later new crystal structures and protein sequences show that the less common periodicities envisaged by Pauling also occur in coiled coils, adding a variant packing mode ('knobs-to-knobs') to the standard model. Pauling's laboratory notebooks suggest that he searched unsuccessfully for this packing mode in 1953.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreas, Michael P.; Ajay, Gautam; Gellings, Jaclyn A.

X-ray structural determination of segments of the myosin rod has proved difficult because of the strong salt-dependent aggregation properties and repeating pattern of charges on the surface of the coiled-coil that lead to the formation of paracrystals. This problem has been resolved in part through the use of globular assembly domains that improve protein folding and prevent aggregation. The primary consideration now in designing coiled-coil fusion constructs for myosin is deciding where to truncate the coiled-coil and which amino acid residues to include from the folding domain. This is especially important for myosin that contains numerous regions of low predictedmore » coiled-coil propensity. Here we describe the strategy adopted to determine the structure of the region that extends from Arg1677 – Leu1797 that included two areas that do not show a strong sequence signature of a conventional left-handed coiled coil or canonical heptad repeat. This demonstrates again that, with careful choice of fusion constructs, overlapping structures exhibit very similar conformations for the myosin rod fragments in the canonical regions. However, conformational variability is seen around Leu1706 which is a hot spot for cardiomyopathy mutations suggesting that this might be important for function.« less

Synthesis, characterisation and applications of coiled carbon nanotubes.

PubMed

Hanus, Monica J; Harris, Andrew T

2010-04-01

Coiled carbon nanotubes are helical carbon structures formed when heptagonal and pentagonal rings are inserted into the hexagonal backbone of a 'straight' nanotube. Coiled carbon nanotubes have been reported with both regular and irregular helical structures. In this work the structure, growth mechanism(s), synthesis, properties and potential applications of coiled carbon nanotubes are reviewed. Published data suggests that coiled carbon nanotube synthesis occurs due to nonuniform extrusion of carbon from a catalyst surface. To date, coiled carbon nanotubes have been synthesised using catalyst modification techniques including: (i) the addition of S or P containing compounds during synthesis; (ii) the use of binary or ternary metal catalysts; (iii) the use of microwaves to create a local temperature gradient around individual catalyst particles and; (iv) the use of pH control during catalyst preparation. In most instances coiled carbon nanotubes are produced as a by-product; high yield and/or large-scale synthesis of coiled carbon nanotubes remains problematic. The qualitative analysis of coiled carbon nanotubes is currently hindered by the absence of specific characterisation data in the literature, e.g., oxidation profiles measured by thermogravimetric analysis and Raman spectra of pure coiled carbon nanotube samples.

Coiled-coil intermediate filament stutter instability and molecular unfolding.

PubMed

Arslan, Melis; Qin, Zhao; Buehler, Markus J

2011-05-01

Intermediate filaments (IFs) are the key components of cytoskeleton in eukaryotic cells and are critical for cell mechanics. The building block of IFs is a coiled-coil alpha-helical dimer, consisting of several domains that include linkers and other structural discontinuities. One of the discontinuities in the dimer's coiled-coil region is the so-called 'stutter' region. The stutter is a region where a variation of the amino acid sequence pattern from other parts of the alpha-helical domains of the protein is found. It was suggested in earlier works that due to this sequence variation, the perfect coiled-coil arrangement ceases to exist. Here, we show using explicit water molecular dynamics and well-tempered metadynamics that for the coil2 domain of vimentin IFs the stutter is more stable in a non-alpha-helical, unfolded state. This causes a local structural disturbance in the alpha helix, which has a global effect on the nanomechanics of the structure. Our analysis suggests that the stutter features an enhanced tendency to unfolding even under the absence of external forces, implying a much greater structural instability than previously assumed. As a result it features a smaller local bending stiffness than other segments and presents a seed for the initiation of molecular bending and unfolding at large deformation.

Biomaterials Made from Coiled-Coil Peptides.

PubMed

Conticello, Vincent; Hughes, Spencer; Modlin, Charles

The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.

Investigation on Prototype Superconducting Linear Synchronous Motor (LSM) for 600-km/h Wheel-Type Railway

NASA Astrophysics Data System (ADS)

Eom, Beomyong; Lee, Changhyeong; Kim, Seokho; Lee, Changyoung; Yun, Sangwon

The existing wheel-type high-speed railway with a rotatable motor has a limit of 600 km/h speed. The normal conducting electromagnet has several disadvantages to realize 600 km/h speed. Several disadvantages are the increased space and weight, and the decreased electric efficiency to generate the required high magnetic field. In order to reduce the volume and weight, superconducting electromagnets can be considered for LSM (Linear Synchronous Motor). Prior to the fabrication of the real system, a prototype demo-coil is designed and fabricated using 2G high temperature superconducting wire. The prototype HTS coil is cooled by the conduction using a GM cryocooler. To reduce the heat penetration, thermal design was performed for the current leads, supporting structure and radiation shield considering the thermal stress. The operating temperature and current are 30∼40 K and 100 A. The coil consists of two double pancake coils (N, S pole, respectively) and it is driven on a test rail, which is installed for the test car. This paper describes the design and test results of the prototype HTS LSM system. Thermal characteristics are investigated with additional dummy thermal mass on the coil after turning off the cryocooler.

Misalignment tolerable coil structure for biomedical applications with wireless power transfer.

PubMed

Chow, Jeff P W; Chen, Nan; Chung, Henry S H; Chan, Leanne L H

2013-01-01

Coil-misalignment is one of the major hurdles for inductively coupled wireless power transfer in applications like retinal prosthesis. Weak magnetic flux linkage due to coil misalignments would significantly impair the power efficiency. A novel receiver configuration with high misalignment tolerance is presented in this paper. The proposed receiver is composed of two receiver coils placed orthogonally, so as to reduce the variation of mutual inductance between transmitting and receiving coils under misalignment conditions. Three different receiver coil structures are analyzed and compared using the same length of wire. Theoretical predictions have been confirmed with measurement results.

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids

PubMed Central

Sales, Mark; Plecs, Joseph J.; Holton, James M.; Alber, Tom

2007-01-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed metal binding site to coordinate a single Yb2+ ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Å. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures. PMID:17766380

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

PubMed

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Coil Welding Aid

NASA Technical Reports Server (NTRS)

Wiesenbach, W. T.; Clark, M. C.

1983-01-01

Positioner holds coil inside cylinder during tack welding. Welding aid spaces turns of coil inside cylinder and applies contact pressure while coil is tack-welded to cylinder. Device facilitates fabrication of heat exchangers and other structures by eliminating hand-positioning and clamping of individual coil turns.

In vitro study of near-wall flow in a cerebral aneurysm model with and without coils.

PubMed

Goubergrits, L; Thamsen, B; Berthe, A; Poethke, J; Kertzscher, U; Affeld, K; Petz, C; Hege, H-C; Hoch, H; Spuler, A

2010-09-01

Coil embolization procedures change the flow conditions in the cerebral aneurysm and, therefore, in the near-wall region. Knowledge of these flow changes may be helpful to optimize therapy. The goal of this study was to investigate the effect of the coil-packing attenuation on the near-wall flow and its variability due to differences in the coil structure. An enlarged transparent model of an ACA aneurysm was fabricated on the basis of CT angiography. The near-wall flow was visualized by using a recently proposed technique called Wall-PIV. Coil-packing attenuation of 10%, 15%, and 20% were investigated and compared with an aneurysmal flow without coils. Then the flow variability due to the coil introduction was analyzed in 10 experiments by using a packing attenuation of 15%. A small packing attenuation of 10% already alters the near-wall flow significantly in a large part of the aneurysmal sac. These flow changes are characterized by a slow flow with short (interrupted) path lines. An increased packing attenuation expands the wall area exposed to the altered flow conditions. This area, however, depends on the coil position and/or on the 3D coil structure in the aneurysm. To our knowledge, this is the first time the near-wall flow changes caused by coils in an aneurysm model have been visualized. It can be concluded that future hydrodynamic studies of coil therapy should include an investigation of the coil structure in addition to the coil-packing attenuation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peter H. Titus, et. al.

The ITER vertical stability (VS) coils have been developed through the preliminary design phase by Princeton Plasma Physics Laboratory (PPPL). Final design, prototyping and construction will be carried out by the Chinese Participant Team contributing lab, Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP). The VS coils are a part of the in-vessel coil systems which include edge localized mode (ELM) coils as well as the VS coils. An overview of the ELM coils is provided in another paper at this conference. 15 The VS design employs four turns of stainless steel jacketed mineral insulated copper (SSMIC) conductors Themore » mineral insulation is Magnesium Oxide (MgO). Joule and nuclear heat is removed by water flowing at 3 m/s through the hollow copper conductor. A key element in the design is that slightly elevated temperatures in the conductor and its support spine during operation impose compressive stresses that mitigate fatigue damage. Away from joints, and break-outs, conductor thermal stresses are low because of the axisymmetry of the winding (there are no corner bends as in the ELM coils).The 120 degree segment joint, and break-out or terminal regions are designed with similar but imperfect constraint compared with the ring coil portion of the VS. The support for the break-out region is made from a high strength copper alloy, CuCrZr. This is needed to conduct nuclear heat to the actively cooled conductor and to the vessel wall. The support "spine" for the ring coil portion of the VS is 316 stainless steel, held to the vessel with preloaded 718 bolts. Lorentz loads resulting from normal operating loads, disruption loads and loads from disruption currents in the support spine shared with vessel, are applied to the VS coil. The transmission of the Lorentz and thermal expansion loads from the "spine" to the vessel rails is via friction augmented with a restraining "lip" to ensure the coil frictional slip is minimal and acceptable. Stresses in the coil, joints, and break-outs are presented. These are compared with static and fatigue allowables. Design for fatigue is much less demanding than for the ELM coils. A total of 30,000 cycles is required for VS design. Loads on the vessel due to the thermal expansion of the coil and spine are significant. Efforts to reduce these by reducing the cross section of the spine have been made but the vessel still must support loads resulting from restraint of thermal expansion.« less

Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein.

PubMed

Royer, William E; Omartian, Michael N; Knapp, James E

2007-01-05

Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16 degrees relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 A resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil "spokes" projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

High-resolution structures of a heterochiral coiled coil

DOE PAGES

Mortenson, David E.; Steinkruger, Jay D.; Kreitler, Dale F.; ...

2015-10-12

Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from D amino acids (D peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein–protein interactions. Coiled–coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled–coil interactions were predicted over 50 years ago by Crick, andmore » limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report in this paper two independent crystal structures that elucidate coiled-coil packing between L- and D-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. Finally, however, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.« less

Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

DOE PAGES

Taylor, Keenan C.; Buvoli, Massimo; Korkmaz, Elif Nihal; ...

2015-07-06

The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report in this paper that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility.more » Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. Finally, in addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.« less

α/β coiled coils

PubMed Central

Hartmann, Marcus D; Mendler, Claudia T; Bassler, Jens; Karamichali, Ioanna; Ridderbusch, Oswin; Lupas, Andrei N; Hernandez Alvarez, Birte

2016-01-01

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold. DOI: http://dx.doi.org/10.7554/eLife.11861.001 PMID:26771248

Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins.

PubMed

Maitip, Jakkrawut; Trueman, Holly E; Kaehler, Benjamin D; Huttley, Gavin A; Chantawannakul, Panuwan; Sutherland, Tara D

2015-04-01

Multiple gene duplication events in the precursor of the Aculeata (bees, ants, hornets) gave rise to four silk genes. Whilst these homologs encode proteins with similar amino acid composition and coiled coil structure, the retention of all four homologs implies they each are important. In this study we identified, produced and characterized the four silk proteins from Apis dorsata, the giant Asian honeybee. The proteins were readily purified, allowing us to investigate the folding behavior of solutions of individual proteins in comparison to mixtures of all four proteins at concentrations where they assemble into their native coiled coil structure. In contrast to solutions of any one protein type, solutions of a mixture of the four proteins formed coiled coils that were stable against dilution and detergent denaturation. The results are consistent with the formation of a heteromeric coiled coil protein complex. The mechanism of silk protein coiled coil formation and evolution is discussed in light of these results. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural features of LC8-induced self-association of swallow.

PubMed

Kidane, Ariam I; Song, Yujuan; Nyarko, Afua; Hall, Justin; Hare, Michael; Löhr, Frank; Barbar, Elisar

2013-09-03

Cell functions depend on the collective activity of protein networks within which a few proteins, called hubs, participate in a large number of interactions. Dynein light chain LC8, first discovered as a subunit of the motor protein dynein, is considered to have a role broader than that of dynein, and its participation in diverse systems fits the description of a hub. Among its partners is Swallow with which LC8 is essential for proper localization of bicoid mRNA at the anterior cortex of Drosophila oocytes. Why LC8 is essential in this process is not clear, but emerging evidence suggests that LC8 functions by promoting self-association and/or structural organization of its diverse binding partners. This work addresses the energetics and structural features of LC8-induced Swallow self-association distant from LC8 binding. Mutational design based on a hypothetical helical wheel, intermonomer nuclear Overhauser effects assigned to residues expected at interface positions, and circular dichroism spectral characteristics indicate that the LC8-promoted dimer of Swallow is a coiled coil. Secondary chemical shifts and (15)N backbone relaxation identify the boundaries and distinguishing structural features of the coiled coil. Thermodynamic analysis of Swallow polypeptides designed to decouple self-association from LC8 binding reveals that the higher binding affinity of the engineered bivalent Swallow is of purely entropic origin and that the linker separating the coiled coil from the LC8 binding site remains disordered. We speculate that the LC8-promoted coiled coil is critical for bicoid mRNA localization because it favors structural organization of Swallow, which except for the central LC8-promoted coiled coil is primarily disordered.

Structural Features of LC8-Induced Self Association of Swallow†

PubMed Central

Kidane, Ariam I.; Song, Yujuan; Nyarko, Afua; Hall, Justin; Hare, Michael; Löhr, Frank; Barbar, Elisar

2013-01-01

Cell function depends on the collective activity of protein networks within which a few proteins, called hubs, participate in a large number of interactions. Dynein light chain LC8, first discovered as a subunit of the motor protein dynein, is considered to have a role broader than dynein and its participation in diverse systems fits the description of a hub. Among its partners is Swallow with which LC8 is essential for proper localization of bicoid mRNA at the anterior cortex of Drosophila oocytes. Why LC8 is essential in this process is not clear, but emerging evidence suggests that LC8 functions by promoting self-association and/or structural organization of its diverse binding partners. This work addresses the mechanistic and structural features of LC8-induced Swallow self-association distant from LC8 binding. Mutational design based on a hypothetical helical wheel, inter-monomer NOEs assigned to residues expected at interface positions and circular dichroism spectral characteristics indicate that the LC8-promoted dimer of Swallow is a coiled-coil. Secondary chemical shifts and 15N backbone relaxation identify the boundaries and distinguishing structural features of the coiled-coil. Thermodynamic analysis of Swallow polypeptides designed to decouple self-association from LC8 binding reveals that the higher binding affinity of the engineered bivalent Swallow is of purely entropic origin and that the linker separating the coiled-coil from the LC8 binding site remains disordered. We speculate that the LC8-promoted coiled-coil is critical for bicoid mRNA localization because it could induce structural organization of Swallow, which except for the central LC8-promoted coiled-coil is primarily disordered. PMID:23914803

Coiled-Coil Irregularities and Instabilities in Group A Streptococcus M1 Are Required for Virulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNamara, Case; Zinkernagel, Annelies S.; Macheboeuf, Pauline

2008-07-21

Antigenically variable M proteins are major virulence factors and immunogens of the human pathogen group A Streptococcus (GAS). Here, we report the -3 angstrom resolution structure of a GAS M1 fragment containing the regions responsible for eliciting type-specific, protective immunity and for binding fibrinogen, which promotes M1 proinflammatory and antiphagocytic functions. The structure revealed substantial irregularities and instabilities throughout the coiled coil of the M1 fragment. Similar structural irregularities occur in myosin and tropomyosin, explaining the patterns of cross-reactivity seen in autoimmune sequelae of GAS infection. Sequence idealization of a large segment of the M1 coiled coil enhanced stability butmore » diminished fibrinogen binding, proinflammatory effects, and antibody cross-reactivity, whereas it left protective immunogenicity undiminished. Idealized M proteins appear to have promise as vaccine immunogens.« less

Dynamic contrast-enhanced breast MRI at 7 Tesla utilizing a single-loop coil: a feasibility trial.

PubMed

Umutlu, Lale; Maderwald, Stefan; Kraff, Oliver; Theysohn, Jens M; Kuemmel, Sherko; Hauth, Elke A; Forsting, Michael; Antoch, Gerald; Ladd, Mark E; Quick, Harald H; Lauenstein, Thomas C

2010-08-01

The aim of this study was to assess the feasibility of dynamic contrast-enhanced ultra-high-field breast imaging at 7 Tesla. A total of 15 subjects, including 5 patients with histologically proven breast cancer, were examined on a 7 Tesla whole-body magnetic resonance imaging system using a unilateral linearly polarized single-loop coil. Subjects were placed in prone position on a biopsy support system, with the coil placed directly below the region of interest. The examination protocol included the following sequences: 1) T2-weighted turbo spin echo sequence; 2) six dynamic T1-weighted spoiled gradient-echo sequences; and 3) subtraction imaging. Contrast-enhanced T1-weighted imaging at 7 Tesla could be obtained at high spatial resolution with short acquisition times, providing good image accuracy and a conclusively good delineation of small anatomical and pathological structures. T2-weighted imaging could be obtained with high spatial resolution at adequate acquisition times. Because of coil limitations, four high-field magnetic resonance examinations showed decreased diagnostic value. This first scientific approach of dynamic contrast-enhanced breast magnetic resonance imaging at 7 Tesla demonstrates the complexity of ultra-high-field breast magnetic resonance imaging and countenances the implementation of further advanced bilateral coil concepts to circumvent current limitations from the coil and ultra-high-field magnetic strength. 2010 AUR. Published by Elsevier Inc. All rights reserved.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed

Burkhard, P; Meier, M; Lustig, A

2000-12-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed Central

Burkhard, P.; Meier, M.; Lustig, A.

2000-01-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system. PMID:11206050

High-Resolution and Frequency, Printed Miniature Magnetic Probes

NASA Astrophysics Data System (ADS)

Prager, James; Ziemba, Timothy; Miller, Kenneth; Picard, Julian

2013-10-01

Eagle Harbor Technologies, Inc. (EHT) is developing a technique to significantly reduce the cost and development time of producing magnetic field diagnostics. EHT is designing probes that can be printed on flexible PCBs thereby allowing for extremely small coils to be produced while essentially eliminating the time to wind the coils. The coil size can be extremely small when coupled with the EHT Hybrid Integrator, which is capable of high bandwidth measurements over short and long pulse durations. This integrator is currently being commercialized with the support of a DOE SBIR. Additionally, the flexible PCBs allow probes to be attached to complex surface and/or probes that have a complex 3D structure to be designed and fabricated. During the Phase I, EHT will design and construct magnetic field probes on flexible PCBs, which will be tested at the University of Washington's HIT-SI experiment and in EHT's material science plasma reactor. Funding provided by DOE SBIR/STTR Program.

Design development and construction of the RFX field shaping winding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chitarin, G.; Guarnieri, M.; Stella, A.

1989-03-01

The paper describes the development work on the design and the manufacture of the RFX Field Shaping Winding, from the preliminary analysis and the tests on prototypes to the final design. The winding consists of 16 coils, with 24 copper turns each and of diameters up to 5.5 m. The maximum current is 6.25 kA and the maximum voltage to earth is 35 kV. Each coil is supported in 24 radial locations and the electrodynamic load on a single coil is approximately 40 kN/m in normal operation. Fiberglass impregnated with epoxy resin, reinforced in places with polymide tape, has beenmore » used for the insulation. The high levels of the electrical and mechanical strength specified present conflicting constraints, which have required some care in the structural design and the definition of insulation system and impregnation technology. Although the use of copper coils with this kid of insulation may seem obvious and well established, indeed the stringent operational requirements have posed a number of problems which have demanded extensive work on the design and prototype development.« less

Design of a Microwave Assisted Discharge Inductive Plasma Accelerator

NASA Technical Reports Server (NTRS)

Hallock, Ashley K.; Polzin, Kurt A.

2010-01-01

The design and construction of a thruster that employs electrodeless plasma preionization and pulsed inductive acceleration is described. Preionization is achieved through an electron cyclotron resonance discharge that produces a weakly-ionized plasma at the face of a conical theta pinch-shaped inductive coil. The presence of the preionized plasma allows for current sheet formation at lower discharge voltages than those employed in other pulsed inductive accelerators that do not employ preionization. The location of the electron cyclotron resonance discharge is controlled through the design of the applied magnetic field in the thruster. Finite element analysis shows that there is an arrangement of permanent magnets that yields a small volume of resonant magnetic field at the coil face. Preionization in the resonant zone leads to current sheet formation at the coil face, which minimizes the initial inductance of the pulse circuit and maximizes the potential electrical efficiency of the accelerator. A magnet assembly was constructed around an inductive coil to provide structural support to the selected arrangement of neodymium magnets. Measured values of the resulting magnetic field compare favorably with the finite element model.

Improved structure and long-life blanket concepts for heliotron reactors

NASA Astrophysics Data System (ADS)

Sagara, A.; Imagawa, S.; Mitarai, O.; Dolan, T.; Tanaka, T.; Kubota, Y.; Yamazaki, K.; Watanabe, K. Y.; Mizuguchi, N.; Muroga, T.; Noda, N.; Kaneko, O.; Yamada, H.; Ohyabu, N.; Uda, T.; Komori, A.; Sudo, S.; Motojima, O.

2005-04-01

New design approaches are proposed for the LHD-type heliotron D-T demo-reactor FFHR2 to solve the key engineering issues of blanket space limitation and replacement difficulty. A major radius of over 14 m is selected to permit a blanket-shield thickness of about 1 m and to reduce the neutron wall loading and toroidal field, while achieving an acceptable cost of electricity. Two sets of optimization are successfully carried out. One is to reduce the magnetic hoop force on the helical coil support structures by adjustment of the helical winding coil pitch parameter and the poloidal coils design, which facilitates expansion of the maintenance ports. The other is a long-life blanket concept using carbon armour tiles that soften the neutron energy spectrum incident on the self-cooled flibe-reduced activation ferritic steel blanket. In this adaptation of the spectral-shifter and tritium breeder blanket (STB) concept a local tritium breeding ratio over 1.2 is feasible by optimized arrangement of the neutron multiplier Be in the carbon tiles, and the radiation shielding of the superconducting magnet coils is also significantly improved. Using constant cross sections of a helically winding shape, the 'screw coaster' concept is proposed to replace in-vessel components such as the STB armour tiles. The key R&D issues for developing the STB concept, such as radiation effects on carbon and enhanced heat transfer of Flibe, are elucidated.

Optimization of output power and transmission efficiency of magnetically coupled resonance wireless power transfer system

NASA Astrophysics Data System (ADS)

Yan, Rongge; Guo, Xiaoting; Cao, Shaoqing; Zhang, Changgeng

2018-05-01

Magnetically coupled resonance (MCR) wireless power transfer (WPT) system is a promising technology in electric energy transmission. But, if its system parameters are designed unreasonably, output power and transmission efficiency will be low. Therefore, optimized parameters design of MCR WPT has important research value. In the MCR WPT system with designated coil structure, the main parameters affecting output power and transmission efficiency are the distance between the coils, the resonance frequency and the resistance of the load. Based on the established mathematical model and the differential evolution algorithm, the change of output power and transmission efficiency with parameters can be simulated. From the simulation results, it can be seen that output power and transmission efficiency of the two-coil MCR WPT system and four-coil one with designated coil structure are improved. The simulation results confirm the validity of the optimization method for MCR WPT system with designated coil structure.

Structure of the WipA protein reveals a novel tyrosine protein phosphatase effector from Legionella pneumophila.

PubMed

Pinotsis, Nikos; Waksman, Gabriel

2017-06-02

Legionnaires' disease is a severe form of pneumonia caused by the bacterium Legionella pneumophila. L. pneumophila pathogenicity relies on secretion of more than 300 effector proteins by a type IVb secretion system. Among these Legionella effectors, WipA has been primarily studied because of its dependence on a chaperone complex, IcmSW, for translocation through the secretion system, but its role in pathogenicity has remained unknown. In this study, we present the crystal structure of a large fragment of WipA, WipA435. Surprisingly, this structure revealed a serine/threonine phosphatase fold that unexpectedly targets tyrosine-phosphorylated peptides. The structure also revealed a sequence insertion that folds into an α-helical hairpin, the tip of which adopts a canonical coiled-coil structure. The purified protein was a dimer whose dimer interface involves interactions between the coiled coil of one WipA molecule and the phosphatase domain of another. Given the ubiquity of protein-protein interaction mediated by interactions between coiled-coils, we hypothesize that WipA can thereby transition from a homodimeric state to a heterodimeric state in which the coiled-coil region of WipA is engaged in a protein-protein interaction with a tyrosine-phosphorylated host target. In conclusion, these findings help advance our understanding of the molecular mechanisms of an effector involved in Legionella virulence and may inform approaches to elucidate the function of other effectors. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Calculation of Eddy Currents In the CTH Vacuum Vessel and Coil Frame

DOE Office of Scientific and Technical Information (OSTI.GOV)

A. Zolfaghari, A. Brooks, A. Michaels, J. Hanson, and G. Hartwell

2012-09-25

Knowledge of eddy currents in the vacuum vessel walls and nearby conducting support structures can significantly contribute to the accuracy of Magnetohydrodynamics (MHD) equilibrium reconstruction in toroidal plasmas. Moreover, the magnetic fields produced by the eddy currents could generate error fields that may give rise to islands at rational surfaces or cause field lines to become chaotic. In the Compact Toroidal Hybrid (CTH) device (R0 = 0.75 m, a = 0.29 m, B ≤ 0.7 T), the primary driver of the eddy currents during the plasma discharge is the changing flux of the ohmic heating transformer. Electromagnetic simulations are usedmore » to calculate eddy current paths and profile in the vacuum vessel and in the coil frame pieces with known time dependent currents in the ohmic heating coils. MAXWELL and SPARK codes were used for the Electromagnetic modeling and simulation. MAXWELL code was used for detailed 3D finite-element analysis of the eddy currents in the structures. SPARK code was used to calculate the eddy currents in the structures as modeled with shell/surface elements, with each element representing a current loop. In both cases current filaments representing the eddy currents were prepared for input into VMEC code for MHD equilibrium reconstruction of the plasma discharge. __________________________________________________« less

FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry.

PubMed

Martin, Douglas S; Fathi, Reza; Mitchison, Timothy J; Gelles, Jeff

2010-03-23

As the smallest and simplest motor enzymes, kinesins have served as the prototype for understanding the relationship between protein structure and mechanochemical function of enzymes in this class. Conventional kinesin (kinesin-1) is a motor enzyme that transports cargo toward the plus end of microtubules by a processive, asymmetric hand-over-hand mechanism. The coiled-coil neck domain, which connects the two kinesin motor domains, contributes to kinesin processivity (the ability to take many steps in a row) and is proposed to be a key determinant of the asymmetry in the kinesin mechanism. While previous studies have defined the orientation and position of microtubule-bound kinesin motor domains, the disposition of the neck coiled-coil remains uncertain. We determined the neck coiled-coil orientation using a multidonor fluorescence resonance energy transfer (FRET) technique to measure distances between microtubules and bound kinesin molecules. Microtubules were labeled with a new fluorescent taxol donor, TAMRA-X-taxol, and kinesin derivatives with an acceptor fluorophore attached at positions on the motor and neck coiled-coil domains were used to reconstruct the positions and orientations of the domains. FRET measurements to positions on the motor domain were largely consistent with the domain orientation determined in previous studies, validating the technique. Measurements to positions on the neck coiled-coil were inconsistent with a radial orientation and instead demonstrated that the neck coiled-coil is parallel to the microtubule surface. The measured orientation provides a structural explanation for how neck surface residues enhance processivity and suggests a simple hypothesis for the origin of kinesin step asymmetry and "limping."

Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation.

PubMed

Passon, Daniel M; Lee, Mihwa; Rackham, Oliver; Stanley, Will A; Sadowska, Agata; Filipovska, Aleksandra; Fox, Archa H; Bond, Charles S

2012-03-27

Proteins of the Drosophila behavior/human splicing (DBHS) family include mammalian SFPQ (PSF), NONO (p54nrb), PSPC1, and invertebrate NONA and Hrp65. DBHS proteins are predominately nuclear, and are involved in transcriptional and posttranscriptional gene regulatory functions as well as DNA repair. DBHS proteins influence a wide gamut of biological processes, including the regulation of circadian rhythm, carcinogenesis, and progression of cancer. Additionally, mammalian DBHS proteins associate with the architectural long noncoding RNA NEAT1 (Menε/β) to form paraspeckles, subnuclear bodies that alter gene expression via the nuclear retention of RNA. Here we describe the crystal structure of the heterodimer of the multidomain conserved region of the DBHS proteins, PSPC1 and NONO. These proteins form an extensively intertwined dimer, consistent with the observation that the different DBHS proteins are typically copurified from mammalian cells, and suggesting that they act as obligate heterodimers. The PSPC1/NONO heterodimer has a right-handed antiparallel coiled-coil that positions two of four RNA recognition motif domains in an unprecedented arrangement on either side of a 20-Å channel. This configuration is supported by a protein:protein interaction involving the NONA/paraspeckle domain, which is characteristic of the DBHS family. By examining various mutants and truncations in cell culture, we find that DBHS proteins require an additional antiparallel coiled-coil emanating from either end of the dimer for paraspeckle subnuclear body formation. These results suggest that paraspeckles may potentially form through self-association of DBHS dimers into higher-order structures.

In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum.

PubMed

Nasir, Muhammad; Ahmad, Nafees; Sieber, Christian M K; Latif, Amir; Malik, Salman Akbar; Hameed, Abdul

2013-09-24

Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation. The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system. Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain.

Magnetic Microhelix Coil Structures

NASA Astrophysics Data System (ADS)

Smith, Elliot J.; Makarov, Denys; Sanchez, Samuel; Fomin, Vladimir M.; Schmidt, Oliver G.

2011-08-01

Together with the well-known ferro- and antiferromagnetic ordering, nature has created a variety of complex helical magnetic configurations. Here, we design and investigate three-dimensional microhelix coil structures that are radial-, corkscrew-, and hollow-bar-magnetized. The magnetization configurations of the differently magnetized coils are experimentally revealed by probing their specific dynamic response to an external magnetic field. Helix coils offer an opportunity to realize microscale geometries of the magnetic toroidal moment, observed so far only in bulk multiferroic materials.

N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

PubMed

Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

2009-09-15

The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

Integrated PET/MR breast cancer imaging: Attenuation correction and implementation of a 16-channel RF coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oehmigen, Mark, E-mail: mark.oehmigen@uni-due.de

Purpose: This study aims to develop, implement, and evaluate a 16-channel radiofrequency (RF) coil for integrated positron emission tomography/magnetic resonance (PET/MR) imaging of breast cancer. The RF coil is designed for optimized MR imaging performance and PET transparency and attenuation correction (AC) is applied for accurate PET quantification. Methods: A 16-channel breast array RF coil was designed for integrated PET/MR hybrid imaging of breast cancer lesions. The RF coil features a lightweight rigid design and is positioned with a spacer at a defined position on the patient table of an integrated PET/MR system. Attenuation correction is performed by generating andmore » applying a dedicated 3D CT-based template attenuation map. Reposition accuracy of the RF coil on the system patient table while using the positioning frame was tested in repeated measurements using MR-visible markers. The MR, PET, and PET/MR imaging performances were systematically evaluated using modular breast phantoms. Attenuation correction of the RF coil was evaluated with difference measurements of the active breast phantoms filled with radiotracer in the PET detector with and without the RF coil in place, serving as a standard of reference measurement. The overall PET/MR imaging performance and PET quantification accuracy of the new 16-channel RF coil and its AC were then evaluated in first clinical examinations on ten patients with local breast cancer. Results: The RF breast array coil provides excellent signal-to-noise ratio and signal homogeneity across the volume of the breast phantoms in MR imaging and visualizes small structures in the phantoms down to 0.4 mm in plane. Difference measurements with PET revealed a global loss and thus attenuation of counts by 13% (mean value across the whole phantom volume) when the RF coil is placed in the PET detector. Local attenuation ranging from 0% in the middle of the phantoms up to 24% was detected in the peripheral regions of the phantoms at positions closer to attenuating hardware structures of the RF coil. The position accuracy of the RF coil on the patient table when using the positioning frame was determined well below 1 mm for all three spatial dimensions. This ensures perfect position match between the RF coil and its three-dimensional attenuation template during the PET data reconstruction process. When applying the CT-based AC of the RF coil, the global attenuation bias was mostly compensated to ±0.5% across the entire breast imaging volume. The patient study revealed high quality MR, PET, and combined PET/MR imaging of breast cancer. Quantitative activity measurements in all 11 breast cancer lesions of the ten patients resulted in increased mean difference values of SUV{sub max} 11.8% (minimum 3.2%; maximum 23.2%) between nonAC images and images when AC of the RF breast coil was applied. This supports the quantitative results of the phantom study as well as successful attenuation correction of the RF coil. Conclusions: A 16-channel breast RF coil was designed for optimized MR imaging performance and PET transparency and was successfully integrated with its dedicated attenuation correction template into a whole-body PET/MR system. Systematic PET/MR imaging evaluation with phantoms and an initial study on patients with breast cancer provided excellent MR and PET image quality and accurate PET quantification.« less

Optimal wireless receiver structure for omnidirectional inductive power transmission to biomedical implants.

PubMed

Gougheri, Hesam Sadeghi; Kiani, Mehdi

2016-08-01

In order to achieve omnidirectional inductive power transmission to biomedical implants, the use of several orthogonal coils in the receiver side (Rx) has been proposed in the past. In this paper, the optimal Rx structure for connecting three orthogonal Rx coils and the power management is found to achieve the maximum power delivered to the load (PDL) in the presence of any Rx coil tilting. Unlike previous works, in which a separate power management has been used for each coil to deliver power to the load, different resonant Rx structures for connecting three Rx coils to a single power management are studied. In simulations, connecting three Rx coils with the diameters of 3 mm, 3.3 mm, and 3.6 mm in series and resonating them with a single capacitor at the operation frequency of 100 MHz led to the maximum PDL for large loads when the implant was tilted for 45o. This optimal Rx structure achieves higher PDL in worst-case scenarios as well as reduces the number of power managements to only one.

Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, Shannon E.; Nguyen, Elaine; Donegan, Rebecca K.

2017-11-01

Glaucoma-associated myocilin is a member of the olfactomedins, a protein family involved in neuronal development and human diseases. Molecular studies of the myocilin N-terminal coiled coil demonstrate a unique tripartite architecture: a Y-shaped parallel dimer-of-dimers with distinct tetramer and dimer regions. The structure of the dimeric C-terminal 7-heptad repeats elucidates an unexpected repeat pattern involving inter-strand stabilization by oppositely charged residues. Molecular dynamics simulations reveal an alternate accessible conformation in which the terminal inter-strand disulfide limits the extent of unfolding and results in a kinked configuration. By inference, full-length myocilin is also branched, with two pairs of C-terminal olfactomedin domains.more » Selected variants within the N-terminal region alter the apparent quaternary structure of myocilin but do so without compromising stability or causing aggregation. In addition to increasing our structural knowledge of naturally occurring extracellular coiled coils and biomedically important olfactomedins, this work broadens the scope of protein misfolding in the pathogenesis of myocilin-associated glaucoma.« less

Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin.

PubMed

Hill, Shannon E; Nguyen, Elaine; Donegan, Rebecca K; Patterson-Orazem, Athéna C; Hazel, Anthony; Gumbart, James C; Lieberman, Raquel L

2017-11-07

Glaucoma-associated myocilin is a member of the olfactomedins, a protein family involved in neuronal development and human diseases. Molecular studies of the myocilin N-terminal coiled coil demonstrate a unique tripartite architecture: a Y-shaped parallel dimer-of-dimers with distinct tetramer and dimer regions. The structure of the dimeric C-terminal 7-heptad repeats elucidates an unexpected repeat pattern involving inter-strand stabilization by oppositely charged residues. Molecular dynamics simulations reveal an alternate accessible conformation in which the terminal inter-strand disulfide limits the extent of unfolding and results in a kinked configuration. By inference, full-length myocilin is also branched, with two pairs of C-terminal olfactomedin domains. Selected variants within the N-terminal region alter the apparent quaternary structure of myocilin but do so without compromising stability or causing aggregation. In addition to increasing our structural knowledge of naturally occurring extracellular coiled coils and biomedically important olfactomedins, this work broadens the scope of protein misfolding in the pathogenesis of myocilin-associated glaucoma. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dual-cone double-helical downhole logging device

DOEpatents

Yu, Jiunn S.

1984-01-01

A broadband downhole logging device includes a double-helix coil wrapped over a dielectric support and surrounded by a dielectric shield. The device may also include a second coil longitudinally aligned with a first coil and enclosed within the same shield for measuring magnetic permeability of downhole formations and six additional coils for accurately determining downhole parameters.

Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruan, Jianbin; Xu, Chao; Bian, Chuanbing

2012-07-18

We present here the crystal structures of human lamin B1 globular tail domain and coiled 2B domain, which adopt similar folds to Ig-like domain and coiled-coil domain of lamin A, respectively. Despite the overall similarity, we found an extra intermolecular disulfide bond in the lamin B1 coil 2B domain, which does not exist in lamin A/C. In addition, the structural analysis indicates that interactions at the lamin B1 homodimer interface are quite different from those of lamin A/C. Thus our research not only reveals the diversely formed homodimers among lamin family members, but also sheds light on understanding the importantmore » roles of lamin B1 in forming the nuclear lamina matrix.« less

Manufacturing of a REBCO racetrack coil using thermoplastic resin aiming at Maglev application

NASA Astrophysics Data System (ADS)

Mizuno, Katsutoshi; Ogata, Masafumi; Hasegawa, Hitoshi

2015-11-01

The REBCO coated conductor is a promising technology for the Maglev application in terms of its high critical temperature. The operating temperature of the on-board magnets can be around 40-50 K with the coated conductor. The REBCO coils are cooled by cryocoolers directly, and hence the thermal design of the REBCO coils significantly changes from that of LTS coils. We have developed a novel REBCO coil structure using thermoplastic resin. The coil is not impregnated and the thermoplastic resin is used to bond the coil winding and the heat transfer members, e.g. copper and aluminum plates. The viscosity of the thermoplastic resin is high enough for the thermoplastic resin not to permeate between the turns in the coil. Therefore, the thermal stress does not occur and the risk of degradation is removed. This paper contains the following three topics. First, the thermal resistance of the thermoplastic resin was measured at cryogenic temperature. Then, a small round REBCO coil was experimentally produced. It has been confirmed that the thermoplastic resin does not cause the degradation and, the adhesion between the coil winding and copper plates withstands the thermal stress. Finally, we successfully produced a full-scale racetrack REBCO coil applying the coil structure with the thermoplastic resin.

CCBuilder 2.0: Powerful and accessible coiled-coil modeling.

PubMed

Wood, Christopher W; Woolfson, Derek N

2018-01-01

The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Magnetic shielding structure optimization design for wireless power transmission coil

NASA Astrophysics Data System (ADS)

Dai, Zhongyu; Wang, Junhua; Long, Mengjiao; Huang, Hong; Sun, Mingui

2017-09-01

In order to improve the performance of the wireless power transmission (WPT) system, a novel design scheme with magnetic shielding structure on the WPT coil is presented in this paper. This new type of shielding structure has great advantages on magnetic flux leakage reduction and magnetic field concentration. On the basis of theoretical calculation of coil magnetic flux linkage and characteristic analysis as well as practical application feasibility consideration, a complete magnetic shielding structure was designed and the whole design procedure was represented in detail. The simulation results show that the coil with the designed shielding structure has the maximum energy transmission efficiency. Compared with the traditional shielding structure, the weight of the new design is significantly decreased by about 41%. Finally, according to the designed shielding structure, the corresponding experiment platform is built to verify the correctness and superiority of the proposed scheme.

Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles

NASA Astrophysics Data System (ADS)

Shih, Yu-Ling; Le, Trung; Rothfield, Lawrence

2003-06-01

The MinCDE proteins of Escherichia coli are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the E. coli MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in Bacillus subtilis. The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in E. coli and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.

DNA molecules on periodically microstructured lipid membranes: Localization and coil stretching

NASA Astrophysics Data System (ADS)

Hochrein, Marion B.; Leierseder, Judith A.; Golubović, Leonardo; Rädler, Joachim O.

2007-02-01

We explore large scale conformations of DNA molecules adsorbed on curved surfaces. For that purpose, we investigate the behavior of DNA adsorbed on periodically shaped cationic lipid membranes. These unique membrane morphologies are supported on grooved, one-dimensionally periodic microstructured surfaces. Strikingly, we find that these periodically structured membranes are capable to stretch DNA coils. We elucidate this phenomenon in terms of surface curvature dependent potential energy attained by the adsorbed DNA molecules. Due to it, DNA molecules undergo a localization transition causing them to stretch by binding to highly curved sections (edges) of the supported membranes. This effect provides a new venue for controlling conformations of semiflexible polymers such as DNA by employing their interactions with specially designed biocompatible surfaces. We report the first experimental observation of semiflexible polymers unbinding transition in which DNA molecules unbind from one-dimensional manifolds (edges) while remaining bound to two-dimensional manifolds (cationic membranes).

Results of availability imposed configuration details developed for K-DEMO

DOE PAGES

Brown, Tom; Titus, Peter; Brooks, Art; ...

2016-02-05

We completed a two year study using the Korean fusion demonstration reactor (K-DEMO) where we looked at key Tokamak components and configuration options in preparation of a conceptual design phase. A key part of a device configuration centers on defining an arrangement that enhances the ability to reach high availability values by defining design solutions that foster simplified maintenance operations. In order to maximize the size and minimize the number of in-vessel components enlarged TF coils were defined that incorporate a pair of windings within each coil to mitigate pressure drop issues and to reduce the cost of the coils.more » Furthermore, we defined a semi-permanent shield structure in order to develop labyrinth interfaces between double-null plasma contoured shield modules, provide an entity to align blanket components and provide support against disruption loads—with a load path that equilibrates blanket, TF and PF loads through a base structure. Blanket piping services and auxiliary systems that interface with in-vessel components have played a major role in defining the overall device arrangement—concept details will be presented along with general arrangement features and preliminary results obtained from disruption analysis.« less

The dynamics of coiled bodies in the nucleus of adenovirus-infected cells.

PubMed Central

Rebelo, L; Almeida, F; Ramos, C; Bohmann, K; Lamond, A I; Carmo-Fonseca, M

1996-01-01

The coiled body is a specific intranuclear structure of unknown function that is enriched in splicing small nuclear ribonucleoproteins (snRNPs). Because adenoviruses make use of the host cell-splicing machinery and subvert the normal subnuclear organization, we initially decided to investigate the effect of adenovirus infection on the coiled body. The results indicate that adenovirus infection induces the disassembly of coiled bodies and that this effect is probably secondary to the block of host protein synthesis induced by the virus. Furthermore, coiled bodies are shown to be very labile structures, with a half-life of approximately 2 h after treatment of HeLa cells with protein synthesis inhibitors. After blocking of protein synthesis, p80 coilin was detected in numerous microfoci that do not concentrate snRNP. These structures may represent precursor forms of the coiled body, which goes through a rapid cycle of assembly/disassembly in the nucleus and requires ongoing protein synthesis to reassemble. Images PMID:8862526

Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p

PubMed Central

Khazina, Elena

2018-01-01

LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. PMID:29565245

In vivo MR imaging of the human skin at subnanoliter resolution using a superconducting surface coil at 1.5 Tesla.

PubMed

Laistler, Elmar; Poirier-Quinot, Marie; Lambert, Simon A; Dubuisson, Rose-Marie; Girard, Olivier M; Moser, Ewald; Darrasse, Luc; Ginefri, Jean-Christophe

2015-02-01

To demonstrate the feasibility of a highly sensitive superconducting surface coil for microscopic MRI of the human skin in vivo in a clinical 1.5 Tesla (T) scanner. A 12.4-mm high-temperature superconducting coil was used at 1.5T for phantom and in vivo skin imaging. Images were inspected to identify fine anatomical skin structures. Signal-to-noise ratio (SNR) improvement by the high-temperature superconducting (HTS) coil, as compared to a commercial MR microscopy coil was quantified from phantom imaging; the gain over a geometrically identical coil made from copper (cooled or not) was theoretically deduced. Noise sources were identified to evaluate the potential of HTS coils for future studies. In vivo skin images with isotropic 80 μm resolution were demonstrated revealing fine anatomical structures. The HTS coil improved SNR by a factor 32 over the reference coil in a nonloading phantom. For calf imaging, SNR gains of 380% and 30% can be expected over an identical copper coil at room temperature and 77 K, respectively. The high sensitivity of HTS coils allows for microscopic imaging of the skin at 1.5T and could serve as a tool for dermatology in a clinical setting. © 2013 Wiley Periodicals, Inc.

Experimental measurement of coil-rod-coil block copolymer tracer diffusion through entangled coil homopolymers

PubMed Central

Wang, Muzhou; Timachova, Ksenia; Olsen, Bradley D.

2014-01-01

The diffusion of coil-rod-coil triblock copolymers in entangled coil homopolymers is experimentally measured and demonstrated to be significantly slower than rod or coil homopolymers of the same molecular weight. A model coil-rod-coil triblock was prepared by expressing rodlike alanine-rich α-helical polypeptides in E. coli and conjugating coillike poly(ethylene oxide) (PEO) to both ends to form coil-rod-coil triblock copolymers. Tracer diffusion through entangled PEO homopolymer melts was measured using forced Rayleigh scattering at various rod lengths, coil molecular weights, and coil homopolymer concentrations. For rod lengths, L, that are close to the entanglementh length, a, the ratio between triblock diffusivity and coil homopolymer diffusivity decreases monotonically and is only a function of L/a, in quantitative agreement with previous simulation results. For large rod lengths, diffusion follows an arm retraction scaling, which is also consistent with previous theoretical predictions. These experimental results support the key predictions of theory and simulation, suggesting that the mismatch in curvature between rod and coil entanglement tubes leads to the observed diffusional slowing. PMID:25484454

Structural and Biophysical Analysis of BST-2/Tetherin Ectodomains Reveals an Evolutionary Conserved Design to Inhibit Virus Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiecki, M.; Allaire, M.; Scheaffer, S.

2011-01-28

BST-2/tetherin is a host antiviral molecule that functions to potently inhibit the release of enveloped viruses from infected cells. In return, viruses have evolved antagonists to this activity. BST-2 traps budding virions by using two separate membrane-anchoring regions that simultaneously incorporate into the host and viral membranes. Here, we detailed the structural and biophysical properties of the full-length BST-2 ectodomain, which spans the two membrane anchors. The 1.6-{angstrom} crystal structure of the complete mouse BST-2 ectodomain reveals an {approx}145-{angstrom} parallel dimer in an extended {alpha}-helix conformation that predominantly forms a coiled coil bridged by three intermolecular disulfides that are requiredmore » for stability. Sequence analysis in the context of the structure revealed an evolutionarily conserved design that destabilizes the coiled coil, resulting in a labile superstructure, as evidenced by solution x-ray scattering displaying bent conformations spanning 150 and 180 {angstrom} for the mouse and human BST-2 ectodomains, respectively. Additionally, crystal packing analysis revealed possible curvature-sensing tetrameric structures that may aid in proper placement of BST-2 during the genesis of viral progeny. Overall, this extended coiled-coil structure with inherent plasticity is undoubtedly necessary to accommodate the dynamics of viral budding while ensuring separation of the anchors.« less

Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing.

PubMed

Snoberger, Aaron; Brettrager, Evan J; Smith, David M

2018-06-18

Protein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN's symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases' coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.

Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate

PubMed Central

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun; Chang, Changsoo; Joachimiak, Andrzej; Lee, Sukyeong; Tsai, Francis T. F.

2016-01-01

Heat-shock protein of 90 kDa (Hsp90) is an essential molecular chaperone that adopts different 3D structures associated with distinct nucleotide states: a wide-open, V-shaped dimer in the apo state and a twisted, N-terminally closed dimer with ATP. Although the N domain is known to mediate ATP binding, how Hsp90 senses the bound nucleotide and facilitates dimer closure remains unclear. Here we present atomic structures of human mitochondrial Hsp90N (TRAP1N) and a composite model of intact TRAP1 revealing a previously unobserved coiled-coil dimer conformation that may precede dimer closure and is conserved in intact TRAP1 in solution. Our structure suggests that TRAP1 normally exists in an autoinhibited state with the ATP lid bound to the nucleotide-binding pocket. ATP binding displaces the ATP lid that signals the cis-bound ATP status to the neighboring subunit in a highly cooperative manner compatible with the coiled-coil intermediate state. We propose that TRAP1 is a ligand-activated molecular chaperone, which couples ATP binding to dramatic changes in local structure required for protein folding. PMID:26929380

In silico characterization of a novel pathogenic deletion mutation identified in XPA gene in a Pakistani family with severe xeroderma pigmentosum

PubMed Central

2013-01-01

Background Xeroderma Pigmentosum (XP) is a rare skin disorder characterized by skin hypersensitivity to sunlight and abnormal pigmentation. The aim of this study was to investigate the genetic cause of a severe XP phenotype in a consanguineous Pakistani family and in silico characterization of any identified disease-associated mutation. Results The XP complementation group was assigned by genotyping of family for known XP loci. Genotyping data mapped the family to complementation group A locus, involving XPA gene. Mutation analysis of the candidate XP gene by DNA sequencing revealed a novel deletion mutation (c.654del A) in exon 5 of XPA gene. The c.654del A, causes frameshift, which pre-maturely terminates protein and result into a truncated product of 222 amino acid (aa) residues instead of 273 (p.Lys218AsnfsX5). In silico tools were applied to study the likelihood of changes in structural motifs and thus interaction of mutated protein with binding partners. In silico analysis of mutant protein sequence, predicted to affect the aa residue which attains coiled coil structure. The coiled coil structure has an important role in key cellular interactions, especially with DNA damage-binding protein 2 (DDB2), which has important role in DDB-mediated nucleotide excision repair (NER) system. Conclusions Our findings support the fact of genetic and clinical heterogeneity in XP. The study also predicts the critical role of DDB2 binding region of XPA protein in NER pathway and opens an avenue for further research to study the functional role of the mutated protein domain. PMID:24063568

CCBuilder 2.0: Powerful and accessible coiled‐coil modeling

PubMed Central

Wood, Christopher W.

2017-01-01

Abstract The increased availability of user‐friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α‐helical coiled coil provides one such example, which represents ≈ 3–5% of all known protein‐encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy‐to‐use web application, called CCBuilder 2.0, for modeling and optimizing both α‐helical coiled coils and polyproline‐based collagen triple helices. This has many applications from providing models to aid molecular replacement for X‐ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo “dark matter” protein structures. CCBuilder 2.0 is available as a web‐based application, the code for which is open‐source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. Lay Summary We have created CCBuilder 2.0, an easy to use web‐based application that can model structures for a whole class of proteins, the α‐helical coiled coil, which is estimated to account for 3–5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more‐applied research including designing and engineering novel proteins that have potential applications in biotechnology. PMID:28836317

Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terawaki, Shin-ichi, E-mail: terawaki@gunma-u.ac.jp; SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148; Yoshikane, Asuka

Bicaudal-D1 (BICD1) is an α-helical coiled-coil protein mediating the attachment of specific cargo to cytoplasmic dynein. It plays an essential role in minus end-directed intracellular transport along microtubules. The third C-terminal coiled-coil region of BICD1 (BICD1 CC3) has an important role in cargo sorting, including intracellular vesicles associating with the small GTPase Rab6 and the nuclear pore complex Ran binding protein 2 (RanBP2), and inhibiting the association with cytoplasmic dynein by binding to the first N-terminal coiled-coil region (CC1). The crystal structure of BICD1 CC3 revealed a parallel homodimeric coiled-coil with asymmetry and complementary knobs-into-holes interactions, differing from Drosophila BicDmore » CC3. Furthermore, our binding study indicated that BICD1 CC3 possesses a binding surface for two distinct cargos, Rab6 and RanBP2, and that the CC1-binding site overlaps with the Rab6-binding site. These findings suggest a molecular basis for cargo recognition and autoinhibition of BICD proteins during dynein-dependent intracellular retrograde transport. - Highlights: • BICD1 CC3 is a parallel homodimeric coiled-coil with axial asymmetry. • The coiled-coil packing of BICD1 CC3 is adapted to the equivalent heptad position. • BICD1 CC3 has distinct binding sites for two classes of cargo, Rab6 and RanBP2. • The CC1-binding site of BICD1 CC3 overlaps with the Rab6-binding site.« less

Three-axis orthogonal transceiver coil for eddy current sounding

NASA Astrophysics Data System (ADS)

Sukhanov, D.; Zavyalova, K.; Goncharik, M.

2017-08-01

We propose the new structure of three-axis transceiver magnetic-induction coil for eddy current probing. Due to the orientation of the coils, the direct signal from the transmitting coil to the receiving coil is minimized, which provided a high dynamic range. Sensitivity in all directions is provided by combining coils of different orientations. Numerical simulation and experimental studies of such a system have been carried out and confirmed the applicability of the proposed method and the mathematical model.

The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Dental MRI using a dedicated RF-coil at 3 Tesla.

PubMed

Prager, Marcel; Heiland, Sabine; Gareis, Daniel; Hilgenfeld, Tim; Bendszus, Martin; Gaudino, Chiara

2015-12-01

To assess the benefit of a dedicated surface coil to visualize dental structures in comparison to standard head/neck coil. Measurements were performed using the standard head/neck coil and a dedicated array coil for dental MRI at 3 T. As MRI methods, we used a T1-weighted spin-echo sequence with and without spectral fat saturation, a T2-weighted turbo-spin-echo sequence and a 3-dimensional T2-weighted SPACE sequence. Measurements were performed in a phantom to examine sensitivity profiles. Then the signal gain in dental structures was examined in volunteers and in a patient. As expected for a surface coil, the signal gain of the dental coil was highest at the surface of the phantom and decreased with increasing distance to the coil; it was >120% even at a depth of 30 mm, measured from the centre of the coil. The signal gain within the pulp of the volunteers ranged between 236 and 413%. The dedicated array coil offers a significantly higher signal within the region of interest for dental MR imaging thus allowing for better depiction of pathologies within the periodontium and for delineation and tracking of the branches of the maxillary and mandibular nerves. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Understanding Peptide Oligomeric State in Langmuir Monolayers of Amphiphilic 3-Helix Bundle-Forming Peptide-PEG Conjugates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lund, Reidar; Ang, JooChuan; Shu, Jessica Y.

Coiled-coil peptide-polymer conjugates are an emerging class of biomaterials. Fundamental understanding of the coiled-coil oligomeric state and assembly process of these hybrid building blocks is necessary to exert control over their assembly into well-defined structures. Here in this paper, we studied the effect of peptide structure and PEGylation on the self-assembly process and oligomeric state of a Langmuir monolayer of amphiphilic coiled-coil peptide-polymer conjugates using X-ray reflectivity (XR) and grazing-incidence X-ray diffraction (GIXD). Our results show that the oligomeric state of PEGylated amphiphiles based on 3-helix bundle-forming peptide is surface pressure dependent, a mixture of dimers and trimers was formedmore » at intermediate surface pressure but transitions into trimers completely upon increasing surface pressure. Moreover, the interhelical distance within the coiled-coil bundle of 3-helix peptide-PEG conjugate amphiphiles was not perturbed under high surface pressure. Present studies provide valuable insights into the self-assembly process of hybrid peptide-polymer conjugates and guidance to develop biomaterials with controlled multivalency of ligand presentation.« less

Understanding Peptide Oligomeric State in Langmuir Monolayers of Amphiphilic 3-Helix Bundle-Forming Peptide-PEG Conjugates

DOE PAGES

Lund, Reidar; Ang, JooChuan; Shu, Jessica Y.; ...

2016-10-26

Coiled-coil peptide-polymer conjugates are an emerging class of biomaterials. Fundamental understanding of the coiled-coil oligomeric state and assembly process of these hybrid building blocks is necessary to exert control over their assembly into well-defined structures. Here in this paper, we studied the effect of peptide structure and PEGylation on the self-assembly process and oligomeric state of a Langmuir monolayer of amphiphilic coiled-coil peptide-polymer conjugates using X-ray reflectivity (XR) and grazing-incidence X-ray diffraction (GIXD). Our results show that the oligomeric state of PEGylated amphiphiles based on 3-helix bundle-forming peptide is surface pressure dependent, a mixture of dimers and trimers was formedmore » at intermediate surface pressure but transitions into trimers completely upon increasing surface pressure. Moreover, the interhelical distance within the coiled-coil bundle of 3-helix peptide-PEG conjugate amphiphiles was not perturbed under high surface pressure. Present studies provide valuable insights into the self-assembly process of hybrid peptide-polymer conjugates and guidance to develop biomaterials with controlled multivalency of ligand presentation.« less

The Postsynaptic Density Proteins Homer and Shank Form a Polymeric Network Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayashi, M.; Tang, C; Verpelli, C

2009-01-01

The postsynaptic density (PSD) is crucial for synaptic functions, but the molecular architecture retaining its structure and components remains elusive. Homer and Shank are among the most abundant scaffolding proteins in the PSD, working synergistically for maturation of dendritic spines. Here, we demonstrate that Homer and Shank, together, form a mesh-like matrix structure. Crystallographic analysis of this region revealed a pair of parallel dimeric coiled coils intercalated in a tail-to-tail fashion to form a tetramer, giving rise to the unique configuration of a pair of N-terminal EVH1 domains at each end of the coiled coil. In neurons, the tetramerization ismore » required for structural integrity of the dendritic spines and recruitment of proteins to synapses. We propose that the Homer-Shank complex serves as a structural framework and as an assembly platform for other PSD proteins.« less

Potential damage to dc superconducting magnets due to high frequency electromagnetic waves

NASA Technical Reports Server (NTRS)

Gabriel, G. J.; Burkhart, J. A.

1977-01-01

Studies of a d.c. superconducting magnet coil indicate that the large coil behaves as a straight waveguide structure. Voltages between layers within the coil sometimes exceeded those recorded at terminals where protective resistors are located. Protection of magnet coils against these excessive voltages could be accomplished by impedance matching throughout the coil system. The wave phenomenon associated with superconducting magnetic coils may create an instability capable of converting the energy of a quiescent d.c. superconducting coil into dissipative a.c. energy, even in cases when dielectric breakdown does not take place.

Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance1[OPEN

PubMed Central

Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John

2017-01-01

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery. PMID:27879387

Model for the architecture of caveolae based on a flexible, net-like assembly of Cavin1 and Caveolin discs

PubMed Central

Stoeber, Miriam; Schellenberger, Pascale; Siebert, C. Alistair; Leyrat, Cedric; Helenius, Ari

2016-01-01

Caveolae are invaginated plasma membrane domains involved in mechanosensing, signaling, endocytosis, and membrane homeostasis. Oligomers of membrane-embedded caveolins and peripherally attached cavins form the caveolar coat whose structure has remained elusive. Here, purified Cavin1 60S complexes were analyzed structurally in solution and after liposome reconstitution by electron cryotomography. Cavin1 adopted a flexible, net-like protein mesh able to form polyhedral lattices on phosphatidylserine-containing vesicles. Mutating the two coiled-coil domains in Cavin1 revealed that they mediate distinct assembly steps during 60S complex formation. The organization of the cavin coat corresponded to a polyhedral nano-net held together by coiled-coil segments. Positive residues around the C-terminal coiled-coil domain were required for membrane binding. Purified caveolin 8S oligomers assumed disc-shaped arrangements of sizes that are consistent with the discs occupying the faces in the caveolar polyhedra. Polygonal caveolar membrane profiles were revealed in tomograms of native caveolae inside cells. We propose a model with a regular dodecahedron as structural basis for the caveolae architecture. PMID:27834731

Relating the variation of secondary structure of gelatin at fish oil-water interface to adsorption kinetics, dynamic interfacial tension and emulsion stability.

PubMed

Liu, Huihua; Wang, Bo; Barrow, Colin J; Adhikari, Benu

2014-01-15

The objectives of this study were to quantify the relationship between secondary structure of gelatin and its adsorption at the fish-oil/water interface and to quantify the implication of the adsorption on the dynamic interfacial tension (DST) and emulsion stability. The surface hydrophobicity of the gelatin solutions decreased when the pH increased from 4.0 to 6.0, while opposite tend was observed in the viscosity of the solution. The DST values decreased as the pH increased from 4.0 to 6.0, indicating that higher positive charges (measured trough zeta potential) in the gelatin solution tended to result in higher DST values. The adsorption kinetics of the gelatin solution was examined through the calculated diffusion coefficients (Deff). The addition of acid promoted the random coil and β-turn structures at the expense of α-helical structure. The addition of NaOH decreased the β-turn and increased the α-helix and random coil. The decrease in the random coil and triple helix structures in the gelatin solution resulted into increased Deff values. The highest diffusion coefficients, the highest emulsion stability and the lowest amount of random coil and triple helix structures were observed at pH=4.8. The lowest amount of random coil and triple helix structures in the interfacial protein layer correlated with the highest stability of the emulsion (highest ESI value). The lower amount of random coil and triple helix structures allowed higher coverage of the oil-water interface by relatively highly ordered secondary structure of gelatin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Common Evolutionary Origin for the Rotor Domain of Rotary Atpases and Flagellar Protein Export Apparatus

PubMed Central

Kishikawa, Jun-ichi; Ibuki, Tatsuya; Nakamura, Shuichi; Nakanishi, Astuko; Minamino, Tohru; Miyata, Tomoko; Namba, Keiichi; Konno, Hiroki; Ueno, Hiroshi; Imada, Katsumi; Yokoyama, Ken

2013-01-01

The V1- and F1- rotary ATPases contain a rotor that rotates against a catalytic A3B3 or α3β3 stator. The rotor F1-γ or V1-DF is composed of both anti-parallel coiled coil and globular-loop parts. The bacterial flagellar type III export apparatus contains a V1/F1-like ATPase ring structure composed of FliI6 homo-hexamer and FliJ which adopts an anti-parallel coiled coil structure without the globular-loop part. Here we report that FliJ of Salmonella enterica serovar Typhimurium shows a rotor like function in Thermus thermophilus A3B3 based on both biochemical and structural analysis. Single molecular analysis indicates that an anti-parallel coiled-coil structure protein (FliJ structure protein) functions as a rotor in A3B3. A rotary ATPase possessing an F1-γ-like protein generated by fusion of the D and F subunits of V1 rotates, suggesting F1-γ could be the result of a fusion of the genes encoding two separate rotor subunits. Together with sequence comparison among the globular part proteins, the data strongly suggest that the rotor domains of the rotary ATPases and the flagellar export apparatus share a common evolutionary origin. PMID:23724081

Improvement of wireless power transmission efficiency of implantable subcutaneous devices by closed magnetic circuit mechanism.

PubMed

Jo, Sung-Eun; Joung, Sanghoon; Suh, Jun-Kyo Francis; Kim, Yong-Jun

2012-09-01

Induction coils were fabricated based on flexible printed circuit board for inductive transcutaneous power transmission. The coil had closed magnetic circuit (CMC) structure consisting of inner and outer magnetic core. The power transmission efficiency of the fabricated device was measured in the air and in vivo condition. It was confirmed that the CMC coil had higher transmission efficiency than typical air-core coil. The power transmission efficiency during a misalignment between primary coil and implanted secondary coil was also evaluated. The decrease of mutual inductance between the two coils caused by the misalignment led to a low efficiency of the inductive link. Therefore, it is important to properly align the primary coil and implanted secondary coil for effective power transmission. To align the coils, a feedback coil was proposed. This was integrated on the backside of the primary coil and enabled the detection of a misalignment of the primary and secondary coils. As a result of using the feedback coil, the primary and secondary coils could be aligned without knowledge of the position of the implanted secondary coil.

Degradation free epoxy impregnation of REBCO coils and cables

NASA Astrophysics Data System (ADS)

Barth, C.; Bagrets, N.; Weiss, K.-P.; Bayer, C. M.; Bast, T.

2013-05-01

In applications utilizing high-temperature superconductors (HTS) under high mechanical loads as high-field magnets or rotors of generators and motors, the rare-earth-barium-copper-oxide (REBCO) tapes have to be stabilized mechanically. This is achieved using support structures of structural materials and filling the voids in the support through the impregnation of the tapes. The impregnation prevents movement of the tapes and distributes mechanical loads evenly. With high mechanical strengths and low sensitivities to rapid temperature changes, epoxy resins are desired materials for the impregnation of superconductor tapes. However, a strong decrease of the current-carrying capabilities was observed in previous epoxy-impregnated REBCO coils. In this work the thermal expansion mismatches between epoxy resins and REBCO tapes are identified as the cause of these degradations. Fillers are used to reduce the thermal expansions of glues and resins. Mixtures with varying filler contents are analyzed systematically. Their thermal expansions and the corresponding degradations of short REBCO tape samples are measured. A mixture of epoxy resin and filler is found which allows degradation-free impregnation of REBCO tapes. This mixture is validated on a 1.2 m long 15 × 5 Roebel-assembled-coated-conductor (RACC) cable from Industrial Research Limited (IRL).

An engineered allosteric switch in leucine-zipper oligomerization.

PubMed

Gonzalez, L; Plecs, J J; Alber, T

1996-06-01

Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide-benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.

Design of High Field Solenoids made of High Temperature Superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartalesi, Antonio; /Pisa U.

2010-12-01

This thesis starts from the analytical mechanical analysis of a superconducting solenoid, loaded by self generated Lorentz forces. Also, a finite element model is proposed and verified with the analytical results. To study the anisotropic behavior of a coil made by layers of superconductor and insulation, a finite element meso-mechanic model is proposed and designed. The resulting material properties are then used in the main solenoid analysis. In parallel, design work is performed as well: an existing Insert Test Facility (ITF) is adapted and structurally verified to support a coil made of YBa{sub 2}Cu{sub 3}O{sub 7}, a High Temperature Superconductormore » (HTS). Finally, a technological winding process was proposed and the required tooling is designed.« less

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

DOE PAGES

Egelman, Edward H.; Xu, C.; DiMaio, F.; ...

2015-01-22

Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure,more » in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.« less

Mechanical performance evaluation of the CFETR central solenoid model coil design

NASA Astrophysics Data System (ADS)

Liu, Xiaogang; Wang, Zhaoliang; Ren, Yong; Li, Junjun; Yin, Dapeng; Li, Lei; Gao, Xiang; Wu, Yu

2018-01-01

The Chinese Fusion Engineering Test Reactor (CFETR) Central Solenoid Model Coil is being fabricated by the Institute of Plasma Physics Chinese Academy of Sciences. The Model Coil is comprised of Nb3Sn and NbTi modules held together by a preload structure. It will operate at 4.5 K to produce a peak field of 12 T at 48 kA. In order to investigate the feasibility and integrity of the Model Coil design before its manufacturing, the mechanical performance has been evaluated for the room temperature preload, 4.5 K stand-by and 48 kA operating conditions. A 1/15 3D detailed model that consists of jackets, insulations, bladders, buffers and preload structure, is constructed and simulated using the coupled structural-thermal-electromagnetic solver of ANSYS. In contrary to a smeared winding pack model, our analysis with the detailed model can directly and precisely simulate the differential thermal contraction effect of the preload structure, jacket and insulations, as well as the electromagnetic load acting on the jacket. The detailed deformation and stress behaviors of the Model Coil are illustrated and discussed. The results indicate that the final design of the CFETR Central Solenoid Model Coil is reasonably conservative and satisfy the design criteria.

Light scattering measurements supporting helical structures for chromatin in solution.

PubMed

Campbell, A M; Cotter, R I; Pardon, J F

1978-05-01

Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

Characterization and optimization of spiral eddy current coils for in-situ crack detection

NASA Astrophysics Data System (ADS)

Mandache, Catalin

2018-03-01

In-situ condition-based maintenance is making strides in the aerospace industry and it is seen as an alternative to scheduled, time-based maintenance. With fatigue cracks originating from fastener holes as the main reason for structural failures, embedded eddy current coils are a viable non-invasive solution for their timely detection. The development and potential broad use of these coils are motivated by a few consistent arguments: (i) inspection of structures of complicated geometries and hard to access areas, that often require disassembly, (ii) alternative to regular inspection actions that could introduce inadvertent damage, (iii) for structures that have short inspection intervals, and (iv) for repaired structures where fastener holes contain bushings and prevent further bolt-hole inspections. Since the spiral coils are aiming at detecting radial cracks emanating from the fastener holes, their design parameters should allow for high inductance, low ohmic losses and power requirements, as well as optimal size and high sensitivity to discontinuities. In this study, flexible, surface conformable, spiral eddy current coils are empirically investigated on mock-up specimens, while numerical analysis is performed for their optimization and design improvement.

Construction and Test Results of Coil 2 of a Three-Coil 800-MHz REBCO Insert for the 1.3-GHz High-Resolution NMR Magnet.

PubMed

Bascuñán, Juan; Michael, Philip; Hahn, Seungyong; Lecrevisse, Thibault; Iwasa, Yukikazu

2017-06-01

This paper focuses on the construction and test results of Coil 2 that is part of a trio of nested coils composing the REBCO 800 MHz insert. Upon its completion, the REBCO 800 MHz insert will be placed in the bore of a 500 MHz low temperature superconducting (LTS) NMR magnet (L500) to form the MIT 1.3 GHz high-resolution NMR magnet. Coil 2 is a stack of 32 double pancake (DP) coils wound with 6-mm wide REBCO tape using the no-insulation (NI) technique. Each pancake is wound on a stainless steel inner supporting ring to prevent the collapsing of its crossover due to the external pressure exerted by the winding pack. Coil 2 will be constructed in the following sequence: 1) after winding each DP will be individually tested in a bath of liquid nitrogen at atmospheric pressure to determine its current carrying capabilities; 2) DPs will be then assembled as a stack with interconnecting joints, and 3) as in Coil 1, each pancake will be overbanded with a stainless steel tape, this time to a thickness of 5 mm, thickness determined by a stress analysis previously performed. Finally the fully assembled Coil 2 will be tested in liquid nitrogen at 77 K and then in liquid helium at 4.2 K. We present here details of the stress analysis leading to the sizing of the DP inner supporting stainless steel ring and of the overbanding thickness required. Test results include coil index, critical current, charging time constant.

Coil End Parts Development Using BEND and Design for MQXF by LARP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Miao; Ambrosio, G.; Bermudez, S. Izquierdo

2016-09-06

End parts are critical components for saddle-shaped coils. They have a structural function where the cables are deformed in order to cross over the magnet aperture. Based on the previous design of the US LARP program for 90 mm aperture quadrupoles (TQ/LQ) and 120 mm aperture quadrupoles (HQ/LHQ) using BEND, the coil ends of the low-β quadruples (MQXF) for the HiLumi LHC upgrade were developed. This paper shows the design of the MQXF coil ends, the analysis of the coil ends during the coil fabrication, the autopsy analysis of the coil ends and the feedback to BEND parameters.

Parametric Study of HTS Coil Quench Protection Strategies

NASA Astrophysics Data System (ADS)

Seibert, Joseph; Zarnstorff, Michael; Zhai, Yuhu

2016-10-01

Next generation fusion devices require high magnetic fields to adequately contain burning plasmas. Use of high temperature superconducting (HTS) coils to generate these magnetic fields would lower energy cost of operation as well as increase stability of the superconducting state compared to low temperature superconducting coils. However, use of HTS coils requires developing quench protection strategies to prevent damage to the coils. One technique involves the utilization of copper discs and other conductors mutually coupled to the HTS coil to quickly extract the current from the coil. Another technique allows conduction between HTS turns to reduce the current in the coil during quench. This project describes a parametric study of the HTS coil and resistive-conductor setup in order to determine limiting cases of the geometry in an attempt to optimize current extraction and coil protection during quench scenarios. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program.

Oncogenic TPM3-ALK activation requires dimerization through the coiled-coil structure of TPM3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amano, Yosuke; Ishikawa, Rie; Sakatani, Toshio

2015-02-13

Inflammatory myofibroblastic tumor (IMT) is a mesenchymal tumor that can arise from anywhere in the body. Anaplastic lymphoma kinase (ALK) gene rearrangements, most often resulting in the tropomyosin 3 (TPM3)-ALK fusion gene, are the main causes of IMT. However, the mechanism of malignant transformation in IMT has yet to be elucidated. The purpose of this study was to clarify the role of the TPM3 region in the transformation of IMT via TPM3-ALK. Lentivirus vectors containing a TPM3-ALK fusion gene lacking various lengths of TPM3 were constructed and expressed in HEK293T and NIH3T3 cell lines. Focus formation assay revealed loss ofmore » contact inhibition in NIH3T3 cells transfected with full-length TPM3-ALK, but not with ALK alone. Blue-native polyacrylamide gel electrophoresis (BN-PAGE) revealed that TPM3-ALK dimerization increased in proportion to the length of TPM3. Western blot showed phosphorylation of ALK, ERK1/2, and STAT3 in HEK293T cells transfected with TPM3-ALK. Thus, the coiled-coil structure of TPM3 contributes to the transforming ability of the TPM3-ALK fusion protein, and longer TPM3 region leads to higher dimer formation. - Highlights: • TPM3-ALK fusion protein dimerizes through the coiled-coil structure of TPM3. • Longer coiled-coil structure of TPM3 leads to higher TPM3-ALK dimer formation. • Presence of TPM3-ALK dimer leads to ALK, STAT3, and ERK1/2 phosphorylation. • Presence of TPM3-ALK leads to loss of contact inhibition. • BN-PAGE is a simple technique for visualizing oncogenic dimerization.« less

A polygonal double-layer coil design for high-efficiency wireless power transfer

NASA Astrophysics Data System (ADS)

Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

2018-05-01

In this work, we present a novel coil structure for the design of Wireless Power Transfer (WPT) systems via magnetic resonant coupling. The new coil consists of two layers of flat polygonal windings in square, pentagonal and hexagonal shapes. The double-layer coil can be conveniently fabricated using the print circuit broad (PCB) technology. In our design, we include an angle between the two layers which can be adjusted to change the area of inter-layer overlap. This unique structure is thoroughly investigated with respect to the quality factor Q and the power transfer efficiency (PTE) using the finite element method (FEM). An equivalent circuit is derived and used to explain the properties of the angularly shifted double-layer coil theoretically. Comparative experiments are conducted from which the performance of the new coil is evaluated quantitatively. Our results have shown that an increased shift angle improves the Q-factor, and the optimal PTE is achieved when the angle reaches the maximum. When compared to the pentagonal and hexagonal coils, the square coil achieves the highest PTE due to its lowest parasitic capacitive effects. In summary, our new coil design improves the performance of WPT systems and allows a formal design procedure for optimization in a given application.

Comprehensive Survey on Improved Focality and Penetration Depth of Transcranial Magnetic Stimulation Employing Multi-Coil Arrays.

PubMed

Wei, Xile; Li, Yao; Lu, Meili; Wang, Jiang; Yi, Guosheng

2017-11-14

Multi-coil arrays applied in transcranial magnetic stimulation (TMS) are proposed to accurately stimulate brain tissues and modulate neural activities by an induced electric field (EF). Composed of numerous independently driven coils, a multi-coil array has alternative energizing strategies to evoke EFs targeting at different cerebral regions. To improve the locating resolution and the stimulating focality, we need to fully understand the variation properties of induced EFs and the quantitative control method of the spatial arrangement of activating coils, both of which unfortunately are still unclear. In this paper, a comprehensive analysis of EF properties was performed based on multi-coil arrays. Four types of planar multi-coil arrays were used to study the relationship between the spatial distribution of EFs and the structure of stimuli coils. By changing coil-driven strategies in a basic 16-coil array, we find that an EF induced by compactly distributed coils decays faster than that induced by dispersedly distributed coils, but the former has an advantage over the latter in terms of the activated brain volume. Simulation results also indicate that the attenuation rate of an EF induced by the 36-coil dense array is 3 times and 1.5 times greater than those induced by the 9-coil array and the 16-coil array, respectively. The EF evoked by the 36-coil dispense array has the slowest decay rate. This result demonstrates that larger multi-coil arrays, compared to smaller ones, activate deeper brain tissues at the expense of decreased focality. A further study on activating a specific field of a prescribed shape and size was conducted based on EF variation. Accurate target location was achieved with a 64-coil array 18 mm in diameter. A comparison between the figure-8 coil, the planar array, and the cap-formed array was made and demonstrates an improvement of multi-coil configurations in the penetration depth and the focality. These findings suggest that there is a tradeoff between attenuation rate and focality in the application of multi-coil arrays. Coil-energizing strategies and array dimensions should be based on an adequate evaluation of these two important demands and the topological structure of target tissues.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng,Y.; Liu, J.; Zheng, Q.

Entry of SARS coronavirus into its target cell requires large-scale structural transitions in the viral spike (S) glycoprotein in order to induce fusion of the virus and cell membranes. Here we describe the identification and crystal structures of four distinct a-helical domains derived from the highly conserved heptad-repeat (HR) regions of the S2 fusion subunit. The four domains are an antiparallel four-stranded coiled coil, a parallel trimeric coiled coil, a four-helix bundle, and a six-helix bundle that is likely the final fusogenic form of the protein. When considered together, the structural and thermodynamic features of the four domains suggest amore » possible mechanism whereby the HR regions, initially sequestered in the native S glycoprotein spike, are released and refold sequentially to promote membrane fusion. Our results provide a structural framework for understanding the control of membrane fusion and should guide efforts to intervene in the SARS coronavirus entry process.« less

The FapF amyloid secretion transporter possesses an atypical asymmetric coiled coil.

PubMed

Rouse, Sarah L; Stylianou, Fisentzos; Grace Wu, H Y; Berry, Jamie-Lee; Sewell, Lee; Morgan, R Marc L; Sauerwein, Andrea C; Matthews, Steve

2018-06-07

Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits, the fibres of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialised outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8 Å resolution. This domain forms a novel asymmetric trimeric coiled-coil that possesses a single buried tyrosine residue as well as a extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail. Copyright © 2018. Published by Elsevier Ltd.

Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).

PubMed

Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

PubMed Central

da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

2013-01-01

Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

Thin film eddy current impulse deicer

NASA Technical Reports Server (NTRS)

Smith, Samuel O.; Zieve, Peter B.

1990-01-01

Two new styles of electrical impulse deicers has been developed and tested in NASA's Icing Research Tunnel. With the Eddy Current Repulsion Deicing Boot (EDB), a thin and flexible spiral coil is encapsulated between two thicknesses of elastomer. The coil, made by an industrial printed circuit board manufacturer, is bonded to the aluminum aircraft leading edge. A capacitor bank is discharged through the coil. Induced eddy currents repel the coil from the aluminum aircraft structure and shed accumulated ice. A second configuration, the Eddy Current Repulsion Deicing-Strip (EDS) uses an outer metal erosion strip fastened over the coil. Opposite flowing eddy currents repel the strip and create the impulse deicing force. The outer strip serves as a surface for the collection and shedding of ice and does not require any structural properties. The EDS is suitable for composite aircraft structures. Both systems successfully dispelled over 95 percent of the accumulated ice from airfoils over the range of the FAA icing envelope.

Magnetic resonance imaging of the inner ear by using a hybrid radiofrequency coil at 7 T

NASA Astrophysics Data System (ADS)

Kim, Kyoung-Nam; Heo, Phil; Kim, Young-Bo; Han, Gyu-Cheol

2015-01-01

Visualization of the membranous structures of the inner ear has been limited to the detection of the normal fluid signal intensity within the bony labyrinth by using magnetic resonance imaging (MRI) equipped with a 1.5 Tesla (T) magnet. High-field (HF) MRI has been available for more than a decade, and numerous studies have documented its significant advantages over conventional MRI with regards to its use in basic scientific research and routine clinical assessments. No previous studies of the inner ear by using HF MRI have been reported, in part because high-quality resolution of mastoid pneumatization is challenging due to artifacts generated in the HF environment and insufficient performance of radiofrequency (RF) coils. Therefore, a hybrid RF coil with integrated circuitry was developed at 7 T and was targeted for anatomical imaging to achieve a high resolution image of the structure of the human inner ear, excluding the bony portion. The inner-ear's structure is composed of soft tissues containing hydrogen ions and includes the membranous labyrinth, endolymphatic space, perilymphatic space, and cochlear-vestibular nerves. Visualization of the inner-ear's anatomy was performed in-vivo with a custom-designed hybrid RF coil and a specific imaging protocol based on an interpolated breath-held examination sequence. The comparative signal intensity value at 30-mm away from the phantom side was 88% higher for the hybrid RF coil and 24% higher for the 8-channel transmit/receive (Tx/Rx) coil than for the commercial birdcage coil. The optimized MRI protocol employed a hybrid RF coil because it enabled high-resolution imaging of the inner-ear's anatomy and accurate mapping of structures including the cochlea and the semicircular canals. These results indicate that 7 T MRI achieves high spatial resolution visualization of the inner-ear's anatomy. Therefore, MRI imaging using a hybrid RF coil at 7 T could provide a powerful tool for clinical investigations of petrous pathologies of the inner ear.

Dynamic allostery of protein alpha helical coiled-coils

PubMed Central

Hawkins, Rhoda J; McLeish, Tom C.B

2005-01-01

Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of ∼2kBT, consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein. PMID:16849225

Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks.

PubMed

Köster, Sarah; Weitz, David A; Goldman, Robert D; Aebi, Ueli; Herrmann, Harald

2015-02-01

Intermediate filament proteins form filaments, fibers and networks both in the cytoplasm and the nucleus of metazoan cells. Their general structural building plan accommodates highly varying amino acid sequences to yield extended dimeric α-helical coiled coils of highly conserved design. These 'rod' particles are the basic building blocks of intrinsically flexible, filamentous structures that are able to resist high mechanical stresses, that is, bending and stretching to a considerable degree, both in vitro and in the cell. Biophysical and computer modeling studies are beginning to unfold detailed structural and mechanical insights into these major supramolecular assemblies of cell architecture, not only in the 'test tube' but also in the cellular and tissue context. Copyright © 2015 Elsevier Ltd. All rights reserved.

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PubMed

Rose, Annkatrin; Schraegle, Shannon J; Stahlberg, Eric A; Meier, Iris

2005-11-16

Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. Mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. Using the coiled-coil prediction program MultiCoil, we have previously identified all long coiled-coil proteins from the model plant Arabidopsis thaliana and have established a searchable Arabidopsis coiled-coil protein database. Here, we have identified all proteins with long coiled-coil domains from 21 additional fully sequenced genomes. Because regions predicted to form coiled-coils interfere with sequence homology determination, we have developed a sequence comparison and clustering strategy based on masking predicted coiled-coil domains. Comparing and grouping all long coiled-coil proteins from 22 genomes, the kingdom-specificity of coiled-coil protein families was determined. At the same time, a number of proteins with unknown function could be grouped with already characterized proteins from other organisms. MultiCoil predicts proteins with extended coiled-coil domains (more than 250 amino acids) to be largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell.

Coiled-coil protein composition of 22 proteomes – differences and common themes in subcellular infrastructure and traffic control

PubMed Central

Rose, Annkatrin; Schraegle, Shannon J; Stahlberg, Eric A; Meier, Iris

2005-01-01

Background Long alpha-helical coiled-coil proteins are involved in diverse organizational and regulatory processes in eukaryotic cells. They provide cables and networks in the cyto- and nucleoskeleton, molecular scaffolds that organize membrane systems and tissues, motors, levers, rotating arms, and possibly springs. Mutations in long coiled-coil proteins have been implemented in a growing number of human diseases. Using the coiled-coil prediction program MultiCoil, we have previously identified all long coiled-coil proteins from the model plant Arabidopsis thaliana and have established a searchable Arabidopsis coiled-coil protein database. Results Here, we have identified all proteins with long coiled-coil domains from 21 additional fully sequenced genomes. Because regions predicted to form coiled-coils interfere with sequence homology determination, we have developed a sequence comparison and clustering strategy based on masking predicted coiled-coil domains. Comparing and grouping all long coiled-coil proteins from 22 genomes, the kingdom-specificity of coiled-coil protein families was determined. At the same time, a number of proteins with unknown function could be grouped with already characterized proteins from other organisms. Conclusion MultiCoil predicts proteins with extended coiled-coil domains (more than 250 amino acids) to be largely absent from bacterial genomes, but present in archaea and eukaryotes. The structural maintenance of chromosomes proteins and their relatives are the only long coiled-coil protein family clearly conserved throughout all kingdoms, indicating their ancient nature. Motor proteins, membrane tethering and vesicle transport proteins are the dominant eukaryote-specific long coiled-coil proteins, suggesting that coiled-coil proteins have gained functions in the increasingly complex processes of subcellular infrastructure maintenance and trafficking control of the eukaryotic cell. PMID:16288662

Microelectromechanical tunable inductor

DOEpatents

Stalford, Harold L [Norman, OK; Hietala, Vincent M [Albuquerque, NM; Fleming, James G [Albuquerque, NM; Fleming, legal representative, Carol

2010-05-04

A microelectromechanical tunable inductor is formed from a pair of substantially-identically-sized coils arranged side by side and coiled up about a central axis which is parallel to a supporting substrate. An in-plane stress gradient is responsible for coiling up the coils which. The inductance provided by the tunable inductor can be electrostatically changed either continuously or in discrete steps using electrodes on the substrate and on each coil. The tunable inductor can be formed with processes which are compatible with conventional IC fabrication so that, in some cases, the tunable inductor can be formed on a semiconductor substrate alongside or on top of an IC.

Systematic size study of an insect antifreeze protein and its interaction with ice.

PubMed

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-02-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations.

Systematic Size Study of an Insect Antifreeze Protein and Its Interaction with Ice

PubMed Central

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-01-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The β-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations. PMID:15713600

Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

PubMed

Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

2012-08-21

Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle: Insight into the Diversity of N-Terminal Recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frye, Jeremiah; Klenchin, Vadim A.; Rayment, Ivan

Tropomyosin is a stereotypical {alpha}-helical coiled coil that polymerizes to form a filamentous macromolecular assembly that lies on the surface of F-actin. The interaction between the C-terminal and N-terminal segments on adjacent molecules is known as the overlap region. We report here two X-ray structures of the chicken smooth muscle tropomyosin overlap complex. A novel approach was used to stabilize the C-terminal and N-terminal fragments. Globular domains from both the human DNA ligase binding protein XRCC4 and bacteriophage {phi}29 scaffolding protein Gp7 were fused to 37 and 28 C-terminal amino acid residues of tropomyosin, respectively, whereas the 29 N-terminal aminomore » acids of tropomyosin were fused to the C-terminal helix bundle of microtubule binding protein EB1. The structures of both the XRCC4 and Gp7 fusion proteins complexed with the N-terminal EB1 fusion contain a very similar helix bundle in the overlap region that encompasses {approx}15 residues. The C-terminal coiled coil opens to allow formation of the helix bundle, which is stabilized by hydrophobic interactions. These structures are similar to that observed in the NMR structure of the rat skeletal overlap complex [Greenfield, N. J., et al. (2006) J. Mol. Biol. 364, 80-96]. The interactions between the N- and C-terminal coiled coils of smooth muscle tropomyosin show significant curvature, which differs somewhat between the two structures and implies flexibility in the overlap complex, at least in solution. This is likely an important attribute that allows tropomyosin to assemble around the actin filaments. These structures provide a molecular explanation for the role of N-acetylation in the assembly of native tropomyosin.« less

Evaluation of CFD Methods for Simulation of Two-Phase Boiling Flow Phenomena in a Helical Coil Steam Generator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pointer, William David; Shaver, Dillon; Liu, Yang

The U.S. Department of Energy, Office of Nuclear Energy charges participants in the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program with the development of advanced modeling and simulation capabilities that can be used to address design, performance and safety challenges in the development and deployment of advanced reactor technology. The NEAMS has established a high impact problem (HIP) team to demonstrate the applicability of these tools to identification and mitigation of sources of steam generator flow induced vibration (SGFIV). The SGFIV HIP team is working to evaluate vibration sources in an advanced helical coil steam generator using computational fluidmore » dynamics (CFD) simulations of the turbulent primary coolant flow over the outside of the tubes and CFD simulations of the turbulent multiphase boiling secondary coolant flow inside the tubes integrated with high resolution finite element method assessments of the tubes and their associated structural supports. This report summarizes the demonstration of a methodology for the multiphase boiling flow analysis inside the helical coil steam generator tube. A helical coil steam generator configuration has been defined based on the experiments completed by Polytecnico di Milano in the SIET helical coil steam generator tube facility. Simulations of the defined problem have been completed using the Eulerian-Eulerian multi-fluid modeling capabilities of the commercial CFD code STAR-CCM+. Simulations suggest that the two phases will quickly stratify in the slightly inclined pipe of the helical coil steam generator. These results have been successfully benchmarked against both empirical correlations for pressure drop and simulations using an alternate CFD methodology, the dispersed phase mixture modeling capabilities of the open source CFD code Nek5000.« less

Invited review the coiled coil silk of bees, ants, and hornets.

PubMed

Sutherland, Tara D; Weisman, Sarah; Walker, Andrew A; Mudie, Stephen T

2012-06-01

In this article, we review current knowledge about the silk produced by the larvae of bees, ants, and hornets [Apoidea and Vespoidea: Hymenoptera]. Different species use the silk either alone or in composites for a variety of purposes including mechanical reinforcement, thermal regulation, or humidification. The characteristic molecular structure of this silk is α-helical proteins assembled into tetrameric coiled coils. Gene sequences from seven species are available, and each species possesses a copy of each of four related silk genes that encode proteins predicted to form coiled coils. The proteins are ordered at multiple length scales within the labial gland of the final larval instar before spinning. The insects control the morphology of the silk during spinning to produce either fibers or sheets. The silk proteins are small and non repetitive and have been produced artificially at high levels by fermentation in E. coli. The artificial silk proteins can be fabricated into materials with structural and mechanical properties similar to those of native silks. Copyright © 2011 Wiley Periodicals, Inc.

Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control.

PubMed

Carroni, Marta; Franke, Kamila B; Maurer, Michael; Jäger, Jasmin; Hantke, Ingo; Gloge, Felix; Linder, Daniela; Gremer, Sebastian; Turgay, Kürşad; Bukau, Bernd; Mogk, Axel

2017-11-22

Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA. ClpC forms large two-helical assemblies that associate via head-to-head contacts between coiled-coil middle domains (MDs). MecA converts this resting state to an active planar ring structure by binding to MD interaction sites. Loss of ClpC repression in MD mutants causes constitutive activation and severe cellular toxicity. These findings unravel an unexpected regulatory concept executed by coiled-coil MDs to tightly control AAA+ chaperone activity.

The asymptotic structure of a slender coiling fluid thread

NASA Astrophysics Data System (ADS)

Blount, Maurice; Lister, John

2010-11-01

The buckling of a viscous fluid thread as it falls through air onto a stationary surface is a well-known breakfast-time phenomenon which exhibits a rich variety of dynamical regimes [1]. Since the bending resistance of a slender thread is small, bending motion is largely confined to a short region of coiling near the surface. If the height of fall is large enough, then the thread above the coiling region forms a `tail' that falls nearly vertically under gravity but is deflected slightly due to forces exerted on it by the coil. Although it is possible to use force balances in the coil to estimate scalings for the coiling frequency, we analyse the solution structure of the entire thread in the asymptotic limit of a very slender thread and thereby include the dynamic interaction between the coil and the tail. Quantitative predictions of the coiling frequency are obtained which demonstrate the existence of leading-order corrections to scalings previously derived. In particular, we show that in the regime where the deflection of the tail is governed by a balance between centrifugal acceleration, hoop stress and gravity, the tail behaves as a flexible circular pendulum that is forced by bending stress exerted by the coil. The amplitude of the response is calculated and the previously observed resonance when the coiling frequency coincides with one of the eigenfrequencies of a free flexible pendulum is thereby explained. [1] N.M. Ribe et al., J. Fluid Mech. 555, 275-297.

Electromagnetic and Mechanical Analysis of the Coil Structure for the CLAS12 Torus for 12 GeV Upgrade

DOE PAGES

Ghoshal, P. K.; Pastor, O.; Kashy, D.; ...

2014-12-18

The torus magnet for the CLAS12 spectrometer is a 3.6 T superconducting magnet being designed and built as part of the Jefferson Lab 12 GeV Upgrade. The magnet consists of six coil case assemblies mounted to a cold central hub. The coil case assembly consists of an aluminum case and cover enclosing an epoxy vacuum impregnated coil pack. The coil pack consists of a 117 turn double-pancake winding wrapped with 2 layers of 0.635 mm thick copper cooling sheets. The coil case assembly is cooled by supercritical helium at 4.6 K. This report details the structural analysis of the coilmore » case assembly and the assessment of the coil pack stresses. For the normal operation of the torus magnet, the coil case assembly was analyzed for cool down to 4.6 K and the Lorentz forces at normal operating current. In addition to the normal operating configuration, the coil case assembly was analyzed for Lorentz forces arising from coil misalignment and current imbalances. The allowable stress criteria for the magnet followed the approach of the ASME codes. Primary stresses were limited to the lesser of 2/3 times the yield strength or 1/3 times the ultimate tensile strength. Primary plus secondary stresses were limited to 3 times the primary stress allowable. The analysis was performed using ANSYS Maxwell to calculate the magneto-static loads and ANSYS Mechanical to calculate the stresses.« less

Crystal structure at 2.8Å of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP-protein interactor (HIPPI)

PubMed Central

Niu, Qian; Ybe, Joel A.

2008-01-01

Summary Huntington’s disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of htt permits HIP-protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits Procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain (DED). Our 2.8 Å crystal structure of the HIP1 371-481 sub-fragment that includes F432 and K474 important for HIPPI binding is not a DED, but is a partially opened coiled-coil. The HIP1 371-481 model reveals a basic surface we hypothesize is suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R from different organisms, but are not conserved in the yeast homolog of HIP1, sla2p. We have modeled ∼85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (PDB code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a “U” shaped HIP1 molecule. PMID:18155047

7-T magnetic resonance imaging of the inner ear's anatomy by using dual four-element radiofrequency coil arrays and the VIBE sequence

NASA Astrophysics Data System (ADS)

Kim, Kyoung-Nam; Heo, Phil; Kim, Young-Bo; Han, Gyu-Cheol

2015-02-01

An ultra-high-field magnetic resonance (MR) scanner and a specially-optimized radiofrequency (RF) coil and sequence protocol are required to obtain high-resolution images of the inner ear that can noninvasively confirm pathologic diagnoses. In phantom studies, the MR signal distribution of the gradient echo MR images generated by using a customized RF coil was compared with that of a commercial volume coil. The MR signal intensity of the customized RF coil decreases rapidly from near the RF coil plane toward the exterior of the phantom. However, the signal sensitivity of this coil is superior on both sides of the phantom, corresponding to the petrous pyramid. In in-vivo 7-T MR imaging, a customized RF coil and a volumetric-interpolated breath-hold examination imaging sequence are employed for visualization of the inner ear's structure. The entire membranous portion of the cochlear and the three semicircular canals, including the ductus reunions, oval window, and round window with associated nervous tissue, were clearly depicted with sufficient spatial coverage for adequate inspection of the surrounding anatomy. Developments from a new perspective to inner ear imaging using the 7-T modality could lead to further improved image sensitivity and, thus, enable ultra-structural MR imaging.

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reinke, Aaron W.; Grant, Robert A.; Keating, Amy E.

2010-06-21

The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein 'interactome' includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of specialmore » interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.« less

Low temperature synthesis of coiled carbon nanotubes and their magnetic properties

NASA Astrophysics Data System (ADS)

Krishna, Vemula Mohana; Somanathan, T.; Manikandan, E.

2018-04-01

In this paper, coiled like structure of carbon nanotubes (c-CNTs) have been effectively grown on bi-metal substituted α-alumina nanoparticles catalyst by chemical vapor deposition (CVD) system. Highly graphitized and dense bundles of carbon product were attained at a low temperature of 550 °C. The coiled carbon nanostructures in very longer lengths were noticed by field emission scanning electron microscope (FESEM) observation. Furthermore, high purity material was achieved, which correlates the energy dispersive x-ray spectroscopy (EDX) analysis. High resolution transmission electron microscope (HRTEM) revealed the diameter and graphitization of coiled structures. The superparamagnetic like behavior was observed at room temperature for the as-synthesized product, which was found by VSM investigation.

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawidziak, Daria M.; Sanchez, Jacint G.; Wagner, Jonathan M.

Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

Opposed slant tube diabatic sorber

DOEpatents

Erickson, Donald C.

2004-01-20

A sorber comprised of at least three concentric coils of tubing contained in a shell with a flow path for liquid sorbent in one direction, a flow path for heat transfer fluid which is in counter-current heat exchange relationship with sorbent flow, a sorbate vapor port in communication with at least one of sorbent inlet or exit ports, wherein each coil is coiled in opposite direction to those coils adjoining it, whereby the opposed slant tube configuration is achieved, with structure for flow modification in the core space inside the innermost coil.

THE STRUCTURES OF COILED-COIL DOMAINS FROM TYPE THREE SECRETION SYSTEM TRANSLOCATORS REVEAL HOMOLOGY TO PORE-FORMING TOXINS

PubMed Central

Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V.

2012-01-01

Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SS) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) which is responsible for over one million deaths per year. The Shigella type III secretion apparatus (T3SA) is comprised of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 Å and 2.8 Å limiting resolution, respectively. These newly identified domains are comprised of extended length (114 Å in IpaB and 71 Å in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably colicin Ia. This suggests that these mechanistically-separate and functionally-distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events. PMID:22321794

The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini

2012-03-26

Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC.more » While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecularmore » envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.« less

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liban, Tyler J.; Medina, Edgar M.; Tripathi, Sarvind

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences formore » different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.« less

Coiled-coil coactivators play a structural role mediating interactions in hypoxia-inducible factor heterodimerization

DOE PAGES

Guo, Yirui; Scheuermann, Thomas H.; Partch, Carrie L.; ...

2015-01-27

The hypoxia-inducible factor complex (HIF-α·aryl hydrocarbon receptor nuclear translocator (ARNT)) requires association with several transcription coactivators for a successful cellular response to hypoxic stress. In addition to the conventional global transcription coactivator CREB-binding protein/p300 (CBP/p300) that binds to the HIF-α transactivation domain, a new group of transcription coactivators called the coiled-coil coactivators (CCCs) interact directly with the second PER-ARNT-SIM (PAS) domain of ARNT (ARNT PAS-B). These less studied transcription coactivators play essential roles in the HIF-dependent hypoxia response, and CCC misregulation is associated with several forms of cancer. To better understand CCC protein recruitment by the heterodimeric HIF transcription factor,more » we used x-ray crystallography, NMR spectroscopy, and biochemical methods to investigate the structure of the ARNT PAS-B domain in complex with the C-terminal fragment of a coiled-coil coactivator protein, transforming acidic coiled-coil coactivator 3 (TACC3). We found that the HIF-2α PAS-B domain also directly interacts with TACC3, motivating an NMR data-derived model suggesting a means by which TACC3 could form a ternary complex with HIF-2α PAS-B and ARNT PAS-B via β-sheet/coiled-coil interactions. Furthermore, these findings suggest that TACC3 could be recruited as a bridge to cooperatively mediate between the HIF-2α PAS-B·ARNT PAS-B complex, thereby participating more directly in HIF-dependent gene transcription than previously anticipated.« less

The kinetochore proteins CENP-E and CENP-F directly and specifically interact with distinct BUB mitotic checkpoint Ser/Thr kinases.

PubMed

Ciossani, Giuseppe; Overlack, Katharina; Petrovic, Arsen; Huis In 't Veld, Pim J; Koerner, Carolin; Wohlgemuth, Sabine; Maffini, Stefano; Musacchio, Andrea

2018-05-10

The segregation of chromosomes during cell division relies on the function of the kinetochores, protein complexes that physically connect chromosomes with microtubules of the spindle. The metazoan proteins, centromere protein E (CENP-E) and CENP-F, are components of a fibrous layer of mitotic kinetochores named the corona. Several of their features suggest that CENP-E and CENP-F are paralogs: they are very large (comprising approximately 2700 and 3200 residues, respectively), contain abundant predicted coiled-coil structures, are C-terminally prenylated, and are endowed with microtubule-binding sites at their termini. Moreover, CENP-E contains an ATP-hydrolyzing motor domain that promotes microtubule plus end-directed motion. Here, we show that both CENP-E and CENP-F are recruited to mitotic kinetochores independently of the main corona constituent, the Rod-Zwilch-ZW10 (RZZ) complex. We identified specific interactions of CENP-F and CENP-E with budding uninhibited by benzimidazole 1 (BUB1) and BUB1-related (BUBR1) mitotic checkpoint Ser/Thr kinases, respectively, paralogous proteins involved in mitotic checkpoint control and chromosome alignment. Whereas BUBR1 was dispensable for kinetochore localization of CENP-E, BUB1 was stringently required for CENP-F localization. Through biochemical reconstitution, we demonstrated that the CENP-E-BUBR1 and CENP-F-BUB1 interactions are direct and require similar determinants, a dimeric coiled-coil in CENP-E or CENP-F and a kinase domain in BUBR1 or BUB1. Our findings are consistent with the existence of structurally similar BUB1-CENP-F and BUBR1-CENP-E complexes, supporting the notion that CENP-E and CENP-F are evolutionarily related. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Conserved tetramer junction in the kinetochore Ndc80 complex

PubMed Central

Valverde, Roberto; Ingram, Jessica; Harrison, Stephen C.

2016-01-01

Summary The heterotetrameric Ndc80 complex establishes connectivity along the principal longitudinal axis of a kinetochore. Its two heterodimeric subcomplexes, each with a globular end and a coiled-coil shaft, connect end-to-end to create a ∼600 Å long rod spanning the gap from centromere-proximal structures to spindle microtubules. Neither subcomplex has a known function on its own, but the heterotetrameric organization and the characteristics of the junction are conserved from yeast to man. We have determined crystal structures of two shortened (“dwarf”) Ndc80 complexes that contain the full tetramer junction and both globular ends. The junction connects two α-helical coiled coils through regions of four-chain and three-chain overlap. The complexity of its structure depends on interactions among conserved amino-acid residues, suggesting a binding site for additional cellular factor(s) not yet identified. PMID:27851957

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solis, S. E.; Centro de Investigacion e Instrumentacion e Imagenologia Medica, Universidad Autonoma Metropolitana Iztapalapa, Mexico, DF 09340; Hernandez, J. A.

Arrays of antennas have been widely accepted for magnetic resonance imaging applications due to their high signal-to-noise ratio (SNR) over large volumes of interest. A new surface coil based on the magnetron tube and called slotted surface coil, has been recently introduced by our group. This coil design experimentally demonstrated a significant improvement over the circular-shaped coil when used in the receive-only mode. The slotted coils formed a two-sheet structure with a 90 deg. separation and each coil had 6 circular slots. Numerical simulations were performed using the finite element method for this coil design to study the behaviour ofmore » the array magnetic field. Then, we developed a two-coil array for brain magnetic resonance imaging to be operated at the resonant frequency of 170 MHz in the transceiver mode. Phantom images were acquired with our coil array and standard pulse sequences on a research-dedicated 4 Tesla scanner. Numerical simulations demonstrated that electromagnetic interaction between the coil elements is negligible, and that the magnetic field showed a good uniformity. In vitro images showed the feasibility of this coil array for standard pulses for high field magnetic resonance imaging.« less

Improving whole brain structural MRI at 4.7 Tesla using 4 irregularly shaped receiver coils.

PubMed

Carmichael, David W; Thomas, David L; De Vita, Enrico; Fernández-Seara, Maria A; Chhina, Navjeet; Cooper, Mark; Sunderland, Colin; Randell, Chris; Turner, Robert; Ordidge, Roger J

2006-09-01

Both higher magnetic field strengths (> or =3 T) and multiple receiver "array coils" can provide increased signal-to-noise ratio (SNR) for MRI. This increase in SNR can be used to obtain images with higher resolution, enabling better visualisation of structures within the human brain. However, high field strength systems also suffer from increased B(1) non-uniformity and increased power deposition, reaching specific absorption rate (SAR) limits more quickly. For these problems to be mitigated, a careful choice of both the pulse sequence design and transmit RF coil is required. This paper describes the use of a prototype array coil consisting of 4 irregularly shaped coils within a standard configuration for neuroimaging at 4.7 T (a head transmit/receive volume coil to minimise SAR and a head gradient insert for maximum gradient performance). With a fast spin echo (FSE) pulse sequence optimised for 4.7 T, this provides dramatically increased quality and resolution over a large brain volume. Using the array coil, a SNR improvement relative to the volume coil of 1-1.5 times in central brain areas and 2-3 times in cortical regions was obtained. Array coil images with a resolution of 352 x 352 x 2000 mum had a SNR of 16.0 to 26.2 in central regions and 19.9 to 34.8 in cortical areas. Such images easily demonstrate cortical myeloarchitecture, while still covering most of the brain in a approximately 12 min scan.

The SENSE-Isomorphism Theoretical Image Voxel Estimation (SENSE-ITIVE) Model for Reconstruction and Observing Statistical Properties of Reconstruction Operators

PubMed Central

Bruce, Iain P.; Karaman, M. Muge; Rowe, Daniel B.

2012-01-01

The acquisition of sub-sampled data from an array of receiver coils has become a common means of reducing data acquisition time in MRI. Of the various techniques used in parallel MRI, SENSitivity Encoding (SENSE) is one of the most common, making use of a complex-valued weighted least squares estimation to unfold the aliased images. It was recently shown in Bruce et al. [Magn. Reson. Imag. 29(2011):1267–1287] that when the SENSE model is represented in terms of a real-valued isomorphism, it assumes a skew-symmetric covariance between receiver coils, as well as an identity covariance structure between voxels. In this manuscript, we show that not only is the skew-symmetric coil covariance unlike that of real data, but the estimated covariance structure between voxels over a time series of experimental data is not an identity matrix. As such, a new model, entitled SENSE-ITIVE, is described with both revised coil and voxel covariance structures. Both the SENSE and SENSE-ITIVE models are represented in terms of real-valued isomorphisms, allowing for a statistical analysis of reconstructed voxel means, variances, and correlations resulting from the use of different coil and voxel covariance structures used in the reconstruction processes to be conducted. It is shown through both theoretical and experimental illustrations that the miss-specification of the coil and voxel covariance structures in the SENSE model results in a lower standard deviation in each voxel of the reconstructed images, and thus an artificial increase in SNR, compared to the standard deviation and SNR of the SENSE-ITIVE model where both the coil and voxel covariances are appropriately accounted for. It is also shown that there are differences in the correlations induced by the reconstruction operations of both models, and consequently there are differences in the correlations estimated throughout the course of reconstructed time series. These differences in correlations could result in meaningful differences in interpretation of results. PMID:22617147

Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI).

PubMed

Niu, Qian; Ybe, Joel A

2008-02-01

Huntington's disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of the huntingtin protein permits HIP1 protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain. Our 2.8-A crystal structure of the HIP1 371-481 subfragment that includes F432 and K474, which is important for HIPPI binding, is not a death-effector domain but is a partially opened coiled coil. The HIP1 371-481 model reveals a basic surface that we hypothesize to be suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R, from different organisms but are not conserved in the yeast homologue of HIP1, sla2p. We have modeled approximately 85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (Protein Data Bank code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a U-shaped HIP1 molecule.

Design of catheter radio frequency coils using coaxial transmission line resonators for interventional neurovascular MR imaging.

PubMed

Zhang, Xiaoliang; Martin, Alastair; Jordan, Caroline; Lillaney, Prasheel; Losey, Aaron; Pang, Yong; Hu, Jeffrey; Wilson, Mark; Cooke, Daniel; Hetts, Steven W

2017-04-01

It is technically challenging to design compact yet sensitive miniature catheter radio frequency (RF) coils for endovascular interventional MR imaging. In this work, a new design method for catheter RF coils is proposed based on the coaxial transmission line resonator (TLR) technique. Due to its distributed circuit, the TLR catheter coil does not need any lumped capacitors to support its resonance, which simplifies the practical design and construction and provides a straightforward technique for designing miniature catheter-mounted imaging coils that are appropriate for interventional neurovascular procedures. The outer conductor of the TLR serves as an RF shield, which prevents electromagnetic energy loss, and improves coil Q factors. It also minimizes interaction with surrounding tissues and signal losses along the catheter coil. To investigate the technique, a prototype catheter coil was built using the proposed coaxial TLR technique and evaluated with standard RF testing and measurement methods and MR imaging experiments. Numerical simulation was carried out to assess the RF electromagnetic field behavior of the proposed TLR catheter coil and the conventional lumped-element catheter coil. The proposed TLR catheter coil was successfully tuned to 64 MHz for proton imaging at 1.5 T. B 1 fields were numerically calculated, showing improved magnetic field intensity of the TLR catheter coil over the conventional lumped-element catheter coil. MR images were acquired from a dedicated vascular phantom using the TLR catheter coil and also the system body coil. The TLR catheter coil is able to provide a significant signal-to-noise ratio (SNR) increase (a factor of 200 to 300) over its imaging volume relative to the body coil. Catheter imaging RF coil design using the proposed coaxial TLR technique is feasible and advantageous in endovascular interventional MR imaging applications.

Nucleolar evolution and coiled bodies during meiotic prophase in Olea europaea: differential localization of nucleic acids.

PubMed

Olmedilla, A; de Dios Alché, J; Rodríguez-García, M I

1997-10-01

We studied the ultrastructural evolution of the nucleolus during meiotic prophase in olive microsporocytes. During prophase, nuclear bodies morphologically similar to coiled bodies were observed. The nucleic acid composition of these bodies was examined in microsporocytes using electron microscopic techniques with EDTA preferential ribonucleoprotein staining, anti-DNA immunolabeling, the in situ terminal deoxynucleotidyl transferase-immunogold technique, and in situ hybridization with 18S rRNA and U3 snoRNA digoxigenin-labeled probes. The ultrastructural appearance of the meiocyte nucleolus indicated a low level of activity from the early prophase stage: the granular component was practically absent and nucleoli were constituted almost exclusively by dense fibrillar component containing large fibrillar centers that lacked chromatin inclusions. However, the appearance of reactivation vacuoles in the nucleolus during zygotene and high levels of rRNA in the nucleoplasm during pachytene support the presence of a peak in rRNA synthesis. Our results also show that the nuclear bodies that appear during prophase I are ribonucleoproteinaceous in nature; neither DNA nor ribosomal RNA were detected. The presence of U3 snoRNA, as shown by in situ hybridization in nuclear bodies from plant material, is also evidence that these structures are coiled bodies. We suggest that coiled bodies are involved not only in pre- and post-splicing events but also in the storage, transport or recycling of rRNA maturation elements.

Potential damage to DC superconducting magnets due to the high frequency electromagnetic waves

NASA Technical Reports Server (NTRS)

Gabriel, G. J.

1977-01-01

Experimental data are presented in support of the hypothesis that a dc superconducting magnet coil does not behave strictly as an inductor, but as a complicated electrodynamic device capable of supporting electromagnetic waves. Travel times of nanosecond pulses and evidence of sinusoidal standing waves were observed on a prototype four-layer solenoidal coil at room temperature. Ringing observed during switching transients appears as a sequence of multiple reflected square pulses whose durations are related to the layer lengths. With sinusoidal excitation of the coil, the voltage amplitude between a pair of points on the coil exhibits maxima at those frequencies such that the distance between these points is an odd multiple of half wavelength in free space. Evidence indicates that any disturbance, such as that resulting from switching or sudden fault, initiates multiple reflections between layers, thus raising the possibility for sufficiently high voltages to cause breakdown.

A study on geometry effect of transmission coil for micro size magnetic induction coil

NASA Astrophysics Data System (ADS)

Lee, Kyung Hwa; Jun, Byoung Ok; Kim, Seunguk; Lee, Gwang Jun; Ryu, Mingyu; Choi, Ji-Woong; Jang, Jae Eun

2016-05-01

The effects of transmission (Tx) coil structure have been studied for micro-size magnetic induction coil. The size of the receiving (Rx) coil should be shrunk to the micrometer level for the various new applications such as micro-robot and wireless body implanted devices. In case of the macro-scale magnetic induction coil, the power transmission efficiency is generally considered to be higher as the inductance of the transmission coil became larger; however, the large size difference between macro-size Tx coil and micro-size Rx coil can decrease the power transmission efficiency due to the difference of resonance frequency. Here, we study a correlation of the power transmission with the size and distance between the macro-size Tx and micro-size Rx coils using magnetic induction technique. The maximum power efficiency was 0.28/0.23/0.13/0.12% at the distance of 0.3/1/3/5 cm between Rx and Tx coil. In addition, more efficient wireless power transferring method is suggested with a floating coil for the body implantable devices. The voltage output increased up to 5.4 mV than the original one Tx coil system. The results demonstrated the foundational wireless power transferring system with enhanced power efficiency.

The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer.

PubMed

Sanchez, Jacint G; Okreglicka, Katarzyna; Chandrasekaran, Viswanathan; Welker, Jordan M; Sundquist, Wesley I; Pornillos, Owen

2014-02-18

Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication.

The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer

PubMed Central

Sanchez, Jacint G.; Okreglicka, Katarzyna; Chandrasekaran, Viswanathan; Welker, Jordan M.; Sundquist, Wesley I.; Pornillos, Owen

2014-01-01

Tripartite motif (TRIM) proteins make up a large family of coiled-coil-containing RING E3 ligases that function in many cellular processes, particularly innate antiviral response pathways. Both dimerization and higher-order assembly are important elements of TRIM protein function, but the atomic details of TRIM tertiary and quaternary structure have not been fully understood. Here, we present crystallographic and biochemical analyses of the TRIM coiled-coil and show that TRIM proteins dimerize by forming interdigitating antiparallel helical hairpins that position the N-terminal catalytic RING domains at opposite ends of the dimer and the C-terminal substrate-binding domains at the center. The dimer core comprises an antiparallel coiled-coil with a distinctive, symmetric pattern of flanking heptad and central hendecad repeats that appear to be conserved across the entire TRIM family. Our studies reveal how the coiled-coil organizes TRIM25 to polyubiquitylate the RIG-I/viral RNA recognition complex and how dimers of the TRIM5α protein are arranged within hexagonal arrays that recognize the HIV-1 capsid lattice and restrict retroviral replication. PMID:24550273

The Whole Elephant: A Synoptic View of Liquid Rope Coiling

NASA Astrophysics Data System (ADS)

Ribe, Neil

2016-11-01

Liquid rope coiling is the instability that occurs when e.g. a thin stream of honey is poured onto toast. While we now have a fine-grained understanding of each of the four principal coiling modes (viscous, gravitational, inertio-gravitational and inertial), we still lack a global view of how the modes cohere to form a larger whole. Using a numerical continuation procedure, I determine how the dimensionless coiling frequency depends on the dimensionless fall height and flow rate, for several values of the dimensionless nozzle diameter. Starting with the onset of coiling, I propose a purely geometrical definition of the critical surface between coiling and no coiling as the locus of points where the radius a1 of the rope at the contact point is just equal to the coil radius R. Coiling with a1 > R is impossible because the rope would intersect itself. I characterize the asymptotic limits of the critical surface as well as the structure of the supercritical volume inside that surface. The procedure reveals a new mode of coiling onset that has not yet been identified.

Fabrication and Optimal Design of Biodegradable Polymeric Stents for Aneurysms Treatments

PubMed Central

Han, Xue; Wu, Xia; Kelly, Michael; Chen, Xiongbiao

2017-01-01

An aneurysm is a balloon-like bulge in the wall of blood vessels, occurring in major arteries of the heart and brain. Biodegradable polymeric stent-assisted coiling is expected to be the ideal treatment of wide-neck complex aneurysms. This paper presents the development of methods to fabricate and optimally design biodegradable polymeric stents for aneurysms treatment. Firstly, a dispensing-based rapid prototyping (DBRP) system was developed to fabricate coil and zigzag structures of biodegradable polymeric stents. Then, compression testing was carried out to characterize the radial deformation of the stents fabricated with the coil or zigzag structure. The results illustrated the stent with a zigzag structure has a stronger radial stiffness than the one with a coil structure. On this basis, the stent with a zigzag structure was chosen for the development of a finite element model for simulating the real compression tests. The result showed the finite element model of biodegradable polymeric stents is acceptable within a range of radial deformation around 20%. Furthermore, the optimization of the zigzag structure was performed with ANSYS DesignXplorer, and the results indicated that the total deformation could be decreased by 35.7% by optimizing the structure parameters, which would represent a significant advance of the radial stiffness of biodegradable polymeric stents. PMID:28264515

Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.

PubMed Central

Wiltscheck, R.; Kammerer, R. A.; Dames, S. A.; Schulthess, T.; Blommers, M. J.; Engel, J.; Alexandrescu, A. T.

1997-01-01

The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

Coiled-Coil Antagonism Regulates Activity of Venus Flytrap-Domain-Containing Sensor Kinases of the BvgS Family

PubMed Central

Lesne, Elodie; Dupré, Elian; Lensink, Marc F.; Locht, Camille

2018-01-01

ABSTRACT Bordetella pertussis controls the expression of its virulence regulon through the two-component system BvgAS. BvgS is a prototype for a family of multidomain sensor kinases. In BvgS, helical linkers connect periplasmic Venus flytrap (VFT) perception domains to a cytoplasmic Per-Arnt-Sim (PAS) domain and the PAS domain to the dimerization/histidine phosphotransfer (DHp) domain of the kinase. The two linkers can adopt coiled-coil structures but cannot do so simultaneously. The first linker forms a coiled coil in the kinase mode and the second in the phosphatase mode, with the other linker in both cases showing an increase in dynamic behavior. The intervening PAS domain changes its quaternary structure between the two modes. In BvgS homologues without a PAS domain, a helical “X” linker directly connects the VFT and DHp domains. Here, we used BvgS as a platform to characterize regulation in members of the PAS-less subfamily. BvgS chimeras of homologues with natural X linkers displayed various regulation phenotypes. We identified two distinct coiled-coil registers in the N- and C-terminal portions of the X linkers. Stable coil formation in the C-terminal moiety determines the phosphatase mode, similarly to BvgS; in contrast, coil formation in the N-terminal moiety along the other register leads to the kinase mode. Thus, antagonism between two registers in the VFT-DHp linker forms the basis for activity regulation in the absence of the PAS domain. The N and C moieties of the X linker play roles similar to those played by the two independent linkers in sensor kinases with a PAS domain, providing a unified mechanism of regulation for the entire family. PMID:29487240

Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin-Garcia, Fernando; Mendieta-Moreno, Jesus Ignacio; Mendieta, Jesus

2012-03-30

Highlights: Black-Right-Pointing-Pointer Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. Black-Right-Pointing-Pointer HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. Black-Right-Pointing-Pointer HRS domains of F protein form three single {alpha}-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmentalmore » pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from {beta}-sheet conformation to an elongated coil and then spontaneously to an {alpha}-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.« less

Bioinformatics study of the mangrove actin genes

NASA Astrophysics Data System (ADS)

Basyuni, M.; Wasilah, M.; Sumardi

2017-01-01

This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

Recent advances in designed coiled coils and helical bundles with inorganic prosthetic groups-from structural to functional applications.

PubMed

Peacock, Anna Fa

2016-04-01

Recent contributions to the de novo design of metalloproteins based on coiled coils and helical bundles are described herein, with examples covering mononuclear, multinuclear, and metallo-porphyrin sites, as well as membrane soluble designs. Important progress is being made in the field with a diverse range of functionalities, sometimes beyond those found in biology, being successfully engineered into these simplified scaffolds and represents an exciting prospect for the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2014-01-29

Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.

Fabrication and Assembly Performance of the First 4.2 m MQXFA Magnet and Mechanical Model for the Hi-Lumi LHC Upgrade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Daniel W.; Ambrosio, Giorgio; Anderssen, Eric C.

Here, the LHC accelerator research program (LARP), in collaboration with CERN and under the scope of the high luminosity upgrade of the Large Hadron Collider, is in the prototyping stage in the development of a 150 mm aperture high-field Nb 3Sn quadrupole magnet called MQXF. This magnet is mechanically supported using a shell-based support structure, which has been extensively demonstrated on several R&D models within LARP, as well as in the more recent short (1.2 m magnetic length) MQXF model program. The MQXFA magnets are each 4.2 m magnetic length, and the first mechanical long model, MQXFA1M (using aluminum surrogatemore » coils), and MQXFAP1 prototype magnet (the first prototype with Nb 3Sn coils) have been assembled at the LBNL. In this paper, we summarize the tooling and the assembly processes, and discuss the mechanical performance of these first two assemblies, comparing strain gauge data with finite element model analysis, as well as the near-term plans for the long MQXF magnet program.« less

Fabrication and Assembly Performance of the First 4.2 m MQXFA Magnet and Mechanical Model for the Hi-Lumi LHC Upgrade

DOE PAGES

Cheng, Daniel W.; Ambrosio, Giorgio; Anderssen, Eric C.; ...

2018-01-30

Here, the LHC accelerator research program (LARP), in collaboration with CERN and under the scope of the high luminosity upgrade of the Large Hadron Collider, is in the prototyping stage in the development of a 150 mm aperture high-field Nb 3Sn quadrupole magnet called MQXF. This magnet is mechanically supported using a shell-based support structure, which has been extensively demonstrated on several R&D models within LARP, as well as in the more recent short (1.2 m magnetic length) MQXF model program. The MQXFA magnets are each 4.2 m magnetic length, and the first mechanical long model, MQXFA1M (using aluminum surrogatemore » coils), and MQXFAP1 prototype magnet (the first prototype with Nb 3Sn coils) have been assembled at the LBNL. In this paper, we summarize the tooling and the assembly processes, and discuss the mechanical performance of these first two assemblies, comparing strain gauge data with finite element model analysis, as well as the near-term plans for the long MQXF magnet program.« less

Structural Analysis of Hand Drawn Bumblebee Bombus terrestris Silk.

PubMed

Woodhead, Andrea L; Sutherland, Tara D; Church, Jeffrey S

2016-07-20

Bombus terrestris, commonly known as the buff-tailed bumblebee, is native to Europe, parts of Africa and Asia. It is commercially bred for use as a pollinator of greenhouse crops. Larvae pupate within a silken cocoon that they construct from proteins produced in modified salivary glands. The amino acid composition and protein structure of hand drawn B. terrestris, silk fibres was investigated through the use of micro-Raman spectroscopy. Spectra were obtained from single fibres drawn from the larvae salivary gland at a rate of 0.14 cm/s. Raman spectroscopy enabled the identification of poly(alanine), poly(alanine-glycine), phenylalanine, tryptophan, and methionine, which is consistent with the results of amino acid analysis. The dominant protein conformation was found to be coiled coil (73%) while the β-sheet content of 10% is, as expected, lower than those reported for hornets and ants. Polarized Raman spectra revealed that the coiled coils were highly aligned along the fibre axis while the β-sheet and random coil components had their peptide carbonyl groups roughly perpendicular to the fibre axis. The protein orientation distribution is compared to those of other natural and recombinant silks. A structural model for the B. terrestris silk fibre is proposed based on these results.

Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.

PubMed

Ohtaki, Akashi; Kida, Hiroshi; Miyata, Yusuke; Ide, Naoki; Yonezawa, Akihiro; Arakawa, Takatoshi; Iizuka, Ryo; Noguchi, Keiichi; Kita, Akiko; Odaka, Masafumi; Miki, Kunio; Yohda, Masafumi

2008-02-29

Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.

A high-precision miniaturized rotating coil transducer for magnetic measurements

DOE PAGES

Arpaia, P.; Buzio, M.; De Oliveira, R.; ...

2018-02-08

A miniaturized Printed Circuit Board (PCB) sensing coil, jointly developed by CERN and Fermilab for measuring the field of small-gap (less than 10 mm) accelerator magnets, is illustrated. A sensing coil array, with a scheme for compensating the main field when measuring the harmonic error components, hosted on a synthetic sapphire-based transducer, is presented. Key innovating features are (i) very-small size, both for the sensing coil array (thickness of 1.380 mm) and for the transducer (overall diameter of 7.350 mm), (ii) metrological performance, namely accuracy (more than five times better than state of the art), and 1-sigma repeatability (ten timesmore » better on harmonics with amplitude less than 100 ppm), and (iii) manufacturing technology of both the coil array (13 double layers aligned within 10 μm), and the sapphire support (concentricity, the most important uncertainty source for rotating coils, 3 μm of uncertainty, namely one order of magnitude better than fiberglass support). After stating the measurement problem, the design of the transducer and a case study of a two-layer PCB sensor array are also illustrated. Then, the prototyping and quality control of both the sensor and the transducer are discussed. Furthermore, the calibration and the results obtained with a prototype setup at Fermilab are presented. Finally, in the appendix, the theory of the rotating coil, the sensor geometry, and the harmonic compensation are briefly reviewed for the reader easiness.« less

A high-precision miniaturized rotating coil transducer for magnetic measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arpaia, P.; Buzio, M.; De Oliveira, R.

A miniaturized Printed Circuit Board (PCB) sensing coil, jointly developed by CERN and Fermilab for measuring the field of small-gap (less than 10 mm) accelerator magnets, is illustrated. A sensing coil array, with a scheme for compensating the main field when measuring the harmonic error components, hosted on a synthetic sapphire-based transducer, is presented. Key innovating features are (i) very-small size, both for the sensing coil array (thickness of 1.380 mm) and for the transducer (overall diameter of 7.350 mm), (ii) metrological performance, namely accuracy (more than five times better than state of the art), and 1-sigma repeatability (ten timesmore » better on harmonics with amplitude less than 100 ppm), and (iii) manufacturing technology of both the coil array (13 double layers aligned within 10 μm), and the sapphire support (concentricity, the most important uncertainty source for rotating coils, 3 μm of uncertainty, namely one order of magnitude better than fiberglass support). After stating the measurement problem, the design of the transducer and a case study of a two-layer PCB sensor array are also illustrated. Then, the prototyping and quality control of both the sensor and the transducer are discussed. Furthermore, the calibration and the results obtained with a prototype setup at Fermilab are presented. Finally, in the appendix, the theory of the rotating coil, the sensor geometry, and the harmonic compensation are briefly reviewed for the reader easiness.« less

MAGNETIC METHOD FOR PRODUCING HIGH VELOCITY SHOCK WAVES IN GASES

DOEpatents

Josephson, V.

1960-01-26

A device is described for producing high-energy plasmas comprising a tapered shock tube of dielectric material and having a closed small end, an exceedingly low-inductance coll supported about and axially aligned with the small end of the tapered tube. an elongated multiturn coil supported upon the remninder of the exterior wall of the shock tube. a potential source and switch connected in series with the low-inductance coil, a potential source and switch connected in series with the elongated coil, means for hermetically sealing the large end of the tube, means for purging the tube of gases, and means for admitting a selected gas into the shock tube.

Drawing-induced changes in morphology and mechanical properties of hornet silk gel films.

PubMed

Kameda, Tsunenori; Kojima, Katsura; Togawa, Eiji; Sezutsu, Hideki; Zhang, Qiang; Teramoto, Hidetoshi; Tamada, Yasushi

2010-04-12

Complete amino acid sequences of the four major proteins (Vssilk 1-4) of silk (hornet silk) obtained from yellow hornet ( Vespa simillima , Vespinae, Vespidae) cocoons have been determined. The native structure of the hornet silk (HS), in which Vssilk 1-4 have an alpha-helix domain with coiled-coil alpha-helices and a beta-sheet domain, is restored when hornet silk gel films (HSGFs) are formed by pressing and drying HS hydrogel. Necking occurs when dry HSGFs are drawn; however, wet HSGFs can be uniaxially drawn with a draw ratio (DR) of 2. Drawing helps obtain high-performance films with a maximum tensile strength and tensile modulus of 170 MPa and 5.5 GPa, respectively. Drawing-induced changes in the orientation and conformation of the coiled-coil structure are investigated.

The ArcB Leucine Zipper Domain Is Required for Proper ArcB Signaling

PubMed Central

Nuñez Oreza, Luis Alberto; Alvarez, Adrián F.; Arias-Olguín, Imilla I.; Torres Larios, Alfredo; Georgellis, Dimitris

2012-01-01

The Arc two-component system modulates the expression of numerous genes in response to respiratory growth conditions. This system comprises ArcA as the response regulator and ArcB as the sensor kinase. ArcB is a tripartite histidine kinase whose activity is regulated by the oxidation of two cytosol-located redox-active cysteine residues that participate in intermolecular disulfide bond formation. Here, we report that the ArcB protein segment covering residues 70–121, fulfills the molecular characteristics of a leucine zipper containing coiled coil structure. Also, mutational analyses of this segment reveal three different phenotypical effects to be distributed along the coiled coil structure of ArcB, demonstrating that this motif is essential for proper ArcB signaling. PMID:22666479

Immobilization of xanthine oxidase on a polyaniline silicone support.

PubMed

Nadruz, W; Marques, E T; Azevedo, W M; Lima-Filho, J L; Carvalho, L B

1996-03-01

A polyaniline silicone support to immobilize xanthine oxidase is proposed as a reactor coil to monitor the action of xanthine oxidase on hypoxanthine, xanthine and 6-mercaptopurine. A purified xanthine oxidase immobilized on this support lost 80% of the initial activity after 12 min of use. Co-immobilization of superoxide dismutase and catalase increased the stability of immobilized xanthine oxidase so that the derivative maintained 79% of its initial activity after 4.6 h of continuous use in which 1.5 mumol purine bases were converted by the immobilized enzyme system. There is no evidence of either polyaniline or protein leaching from the coil during 3 h of continuous use. When solutions (10 ml) of hypoxanthine, xanthine and 6-mercaptopurine were circulated individually through the xanthine oxidase-superoxide dismutase-catalase-polyaniline coil (1 mm internal diameter and 3 m in length, 3 ml internal volume) activities of 8.12, 11.17 and 1.09 nmol min-1 coil-1, respectively, were obtained. The advantages of the reactor configuration and the redox properties of the polymer, particularly with respect to immobilized oxidoreductases, make this methodology attractive for similar enzyme systems. This immobilized enzyme system using polyaniline-silicone as support converted 6-mercaptopurine to 6-thiouric acid with equal efficiency as resins based on polyacrylamide and polyamide 11.

Structure and non-structure of centrosomal proteins.

PubMed

Dos Santos, Helena G; Abia, David; Janowski, Robert; Mortuza, Gulnahar; Bertero, Michela G; Boutin, Maïlys; Guarín, Nayibe; Méndez-Giraldez, Raúl; Nuñez, Alfonso; Pedrero, Juan G; Redondo, Pilar; Sanz, María; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, José M; Gonzalez, Cayetano; Reina, José; Valpuesta, José M; Vernos, Isabelle; Zabala, Juan C; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis

2013-01-01

Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

VP3 is crucial for the stability of Nora virus virions.

PubMed

Sadanandan, Sajna Anand; Ekström, Jens-Ola; Jonna, Venkateswara Rao; Hofer, Anders; Hultmark, Dan

2016-09-02

Nora virus is an enteric virus that causes persistent, non-pathological infection in Drosophila melanogaster. It replicates in the fly gut and is transmitted via the fecal-oral route. Nora virus has a single-stranded positive-sense RNA genome, which is translated in four open reading frames. Reading frame three encodes the VP3 protein, the structure and function of which we have investigated in this work. We have shown that VP3 is a trimer that has an α-helical secondary structure, with a functionally important coiled-coil domain. In order to identify the role of VP3 in the Nora virus life cycle, we constructed VP3-mutants using the cDNA clone of the virus. Our results show that VP3 does not have a role in the actual assembly of the virus particles, but virions that lack VP3 or harbor VP3 with a disrupted coiled coil domain are incapable of transmission via the fecal-oral route. Removing the region downstream of the putative coiled coil appears to have an effect on the fitness of the virus but does not hamper its replication or transmission. We also found that the VP3 protein and particularly the coiled coil domain are crucial for the stability of Nora virus virions when exposed to heat or proteases. Hence, we propose that VP3 is imperative to Nora virus virions as it confers stability to the viral capsid. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Specific arrangement of alpha-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function.

PubMed

Fujii, Takashi; Kato, Takayuki; Namba, Keiichi

2009-11-11

The bacterial flagellar hook is a short, highly curved tubular structure connecting the rotary motor to the filament acting as a helical propeller. The bending flexibility of the hook allows it to work as a universal joint. A partial atomic model of the hook revealed a sliding intersubunit domain interaction along the protofilament to produce bending flexibility. However, it remained unclear how the tightly packed inner core domains can still permit axial extension and compression. We report advances in cryoEM image analysis for high-resolution, high-throughput structural analysis and a density map of the hook that reveals most of the secondary structures, including the terminal alpha helices forming a coiled coil. The orientations and axial packing interactions of these two alpha helices are distinctly different from those of the filament, allowing them to have a room for axial compression and extension for bending flexibility without impairing the mechanical stability of the hook.

Structure and function of the PP2A-shugoshin interaction

PubMed Central

Xu, Zheng; Cetin, Bulent; Anger, Martin; Cho, Uhn Soo; Helmhart, Wolfgang; Nasmyth, Kim; Xu, Wenqing

2009-01-01

SUMMARY Accurate chromosome segregation during mitosis and meiosis depends on shugoshin proteins that prevent precocious dissociation of cohesin from centromeres. Shugoshins associate with PP2A, which is thought to de-phosphorylate cohesin and thereby prevent cleavage by separase during meiosis I. A crystal structure of a complex between a fragment of human Sgo1 and an AB’C PP2A holoenzyme reveals that Sgo1 forms a homodimeric parallel coiled-coil that docks simultaneously onto PP2A’s C and B’ subunits. Sgo1 homo-dimerization is a pre-requisite for PP2A binding. While hSgo1 interacts only with the AB’C holoenzymes, its relative Sgo2 interacts with all PP2A forms and may thus lead to dephosphorylation of distinct substrates. Mutant shugoshin proteins defective in the binding of PP2A cannot protect centromeric cohesin from separase during meiosis I or support the spindle assembly checkpoint in yeast. Finally, we provide evidence that PP2A’s recruitment to chromosomes may be sufficient to protect cohesin from separase in mammalian oocytes. PMID:19716788

Crystal structure of dimeric cardiac L-type calcium channel regulatory domains bridged by Ca[superscript 2+]·calmodulins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fallon, Jennifer L.; Baker, Mariah R.; Xiong, Liangwen

2009-11-10

Voltage-dependent calcium channels (Ca(V)) open in response to changes in membrane potential, but their activity is modulated by Ca(2+) binding to calmodulin (CaM). Structural studies of this family of channels have focused on CaM bound to the IQ motif; however, the minimal differences between structures cannot adequately describe CaM's role in the regulation of these channels. We report a unique crystal structure of a 77-residue fragment of the Ca(V)1.2 alpha(1) subunit carboxyl terminus, which includes a tandem of the pre-IQ and IQ domains, in complex with Ca(2+).CaM in 2 distinct binding modes. The structure of the Ca(V)1.2 fragment is anmore » unusual dimer of 2 coiled-coiled pre-IQ regions bridged by 2 Ca(2+).CaMs interacting with the pre-IQ regions and a canonical Ca(V)1-IQ-Ca(2+).CaM complex. Native Ca(V)1.2 channels are shown to be a mixture of monomers/dimers and a point mutation in the pre-IQ region predicted to abolish the coiled-coil structure significantly reduces Ca(2+)-dependent inactivation of heterologously expressed Ca(V)1.2 channels.« less

Hierarchical Nanostructures Self-Assembled from a Mixture System Containing Rod-Coil Block Copolymers and Rigid Homopolymers

PubMed Central

Li, Yongliang; Jiang, Tao; Lin, Shaoliang; Lin, Jiaping; Cai, Chunhua; Zhu, Xingyu

2015-01-01

Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction εRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the εRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures. PMID:25965726

Dual optimization method of radiofrequency and quasistatic field simulations for reduction of eddy currents generated on 7T radiofrequency coil shielding.

PubMed

Zhao, Yujuan; Zhao, Tiejun; Raval, Shailesh B; Krishnamurthy, Narayanan; Zheng, Hai; Harris, Chad T; Handler, William B; Chronik, Blaine A; Ibrahim, Tamer S

2015-11-01

To optimize the design of radiofrequency (RF) shielding of transmit coils at 7T and reduce eddy currents generated on the RF shielding when imaging with rapid gradient waveforms. One set of a four-element, 2 × 2 Tic-Tac-Toe head coil structure was selected and constructed to study eddy currents on the RF coil shielding. The generated eddy currents were quantitatively studied in the time and frequency domains. The RF characteristics were studied using the finite difference time domain method. Five different kinds of RF shielding were tested on a 7T MRI scanner with phantoms and in vivo human subjects. The eddy current simulation method was verified by the measurement results. Eddy currents induced by solid/intact and simple-structured slotted RF shielding significantly distorted the gradient fields. Echo-planar images, B1+ maps, and S matrix measurements verified that the proposed slot pattern suppressed the eddy currents while maintaining the RF characteristics of the transmit coil. The presented dual-optimization method could be used to design RF shielding and reduce the gradient field-induced eddy currents while maintaining the RF characteristics of the transmit coil. © 2014 Wiley Periodicals, Inc.

The huntingtin interacting protein HIP1 is a clathrin and alpha-adaptin-binding protein involved in receptor-mediated endocytosis.

PubMed

Waelter, S; Scherzinger, E; Hasenbank, R; Nordhoff, E; Lurz, R; Goehler, H; Gauss, C; Sathasivam, K; Bates, G P; Lehrach, H; Wanker, E E

2001-08-15

The huntingtin interacting protein (HIP1) is enriched in membrane-containing cell fractions and has been implicated in vesicle trafficking. It is a multidomain protein containing an N-terminal ENTH domain, a central coiled-coil forming region and a C-terminal actin-binding domain. In the present study we have identified three HIP1 associated proteins, clathrin heavy chain and alpha-adaptin A and C. In vitro binding studies revealed that the central coiled-coil domain is required for the interaction of HIP1 with clathrin, whereas DPF-like motifs located upstream to this domain are important for the binding of HIP1 to the C-terminal 'appendage' domain of alpha-adaptin A and C. Expression of full length HIP1 in mammalian cells resulted in a punctate cytoplasmic immunostaining characteristic of clathrin-coated vesicles. In contrast, when a truncated HIP1 protein containing both the DPF-like motifs and the coiled-coil domain was overexpressed, large perinuclear vesicle-like structures containing HIP1, huntingtin, clathrin and endocytosed transferrin were observed, indicating that HIP1 is an endocytic protein, the structural integrity of which is crucial for maintenance of normal vesicle size in vivo.

Operation Results of the Kstar Helium Refrigeration System

NASA Astrophysics Data System (ADS)

Chang, H.-S.; Fauve, E.; Park, D.-S.; Joo, J.-J.; Moon, K.-M.; Cho, K.-W.; Na, H. K.; Kwon, M.; Yang, S.-H.; Gistau-Baguer, G.

2010-04-01

The "first plasma" (100 kA of controllable plasma current for 100 ms) of KSTAR has been successfully generated in July 2008. The major outstanding feature of KSTAR compared to most other Tokamaks is that all the magnet coils are superconducting (SC), which enables higher plasma current values for a longer time duration when the nominal operation status has been reached. However, to establish the operating condition for the SC coils, other cold components, such as thermal shields, coil-supporting structures, SC buslines, and current leads also must be maintained at proper cryogenic temperature levels. A helium refrigeration system (HRS) with an exergetic equivalent cooling power of 9 kW at 4.5 K has been installed for such purposes and successfully commissioned. In this proceeding, we will report on the operation results of the HRS during the first plasma campaign of KSTAR. Using the HRS, the 300-ton cold mass of KSTAR was cooled down from ambient to the operating temperature levels of each cold component. Stable and steady cryogenic conditions, proper for the generation of the "first plasma" have been maintained for three months, after which, all of the cold mass was warmed up again to ambient temperature.

AC loss modelling and experiment of two types of low-inductance solenoidal coils

NASA Astrophysics Data System (ADS)

Liang, Fei; Yuan, Weijia; Zhang, Min; Zhang, Zhenyu; Li, Jianwei; Venuturumilli, Sriharsha; Patel, Jay

2016-11-01

Low-inductance solenoidal coils, which usually refer to the nonintersecting type and the braid type, have already been employed to build superconducting fault current limiters because of their fast recovery and low inductance characteristics. However, despite their usage there is still no systematical simulation work concerning the AC loss characteristics of the coils built with 2G high temperature superconducting tapes perhaps because of their complicated structure. In this paper, a new method is proposed to simulate both types of coils with 2D axisymmetric models solved by H formulation. Following the simulation work, AC losses of both types of low inductance solenoidal coils are compared numerically and experimentally, which verify that the model works well in simulating non-inductive coils. Finally, simulation works show that pitch has significant impact to AC loss of both types of coils and the inter-layer separation has different impact to the AC loss of braid type of coil in case of different applied currents. The model provides an effective tool for the design optimisation of SFCLs built with non-inductive solenoidal coils.

Design of an interventional magnetic resonance imaging coil for cerebral surgery

NASA Astrophysics Data System (ADS)

Xu, Yue; Wang, Wen-Tao; Wang, Wei-Min

2012-11-01

In clinical magnetic resonance imaging (MRI), the design of the radiofrequency (RF) coil is very important. For certain applications, the appropriate coil can produce an improved image quality. However, it is difficult to achieve a uniform B1 field and a high signal-to-noise ratio (SNR) simultaneously. In this article, we design an interventional transmitter-and-receiver RF coil for cerebral surgery. This coil adopts a disassembly structure that can be assembled and disassembled repeatedly on the cerebral surgery gantry to reduce the amount of interference from the MRI during surgery. The simulation results and the imaging experiments demonstrate that this coil can produce a uniform RF field, a high SNR, and a large imaging range to meet the requirements of the cerebral surgery.

Design of a superconducting 28 GHz ion source magnet for FRIB using a shell-based support structure

DOE PAGES

Felice, H.; Rochepault, E.; Hafalia, R.; ...

2014-12-05

The Superconducting Magnet Program at the Lawrence Berkeley National Laboratory (LBNL) is completing the design of a 28 GHz NbTi ion source magnet for the Facility for Rare Isotope Beams (FRIB). The design parameters are based on the parameters of the ECR ion source VENUS in operation at LBNL since 2002 featuring a sextupole-in-solenoids configuration. Whereas most of the magnet components (such as conductor, magnetic design, protection scheme) remain very similar to the VENUS magnet components, the support structure of the FRIB ion source uses a different concept. A shell-based support structure using bladders and keys is implemented in themore » design allowing fine tuning of the sextupole preload and reversibility of the magnet assembly process. As part of the design work, conductor insulation scheme, coil fabrication processes and assembly procedures are also explored to optimize performance. We present the main features of the design emphasizing the integrated design approach used at LBNL to achieve this result.« less

A combined solenoid-surface RF coil for high-resolution whole-brain rat imaging on a 3.0 Tesla clinical MR scanner.

PubMed

Underhill, Hunter R; Yuan, Chun; Hayes, Cecil E

2010-09-01

Rat brain models effectively simulate a multitude of human neurological disorders. Improvements in coil design have facilitated the wider utilization of rat brain models by enabling the utilization of clinical MR scanners for image acquisition. In this study, a novel coil design, subsequently referred to as the rat brain coil, is described that exploits and combines the strengths of both solenoids and surface coils into a simple, multichannel, receive-only coil dedicated to whole-brain rat imaging on a 3.0 T clinical MR scanner. Compared with a multiturn solenoid mouse body coil, a 3-cm surface coil, a modified Helmholtz coil, and a phased-array surface coil, the rat brain coil improved signal-to-noise ratio by approximately 72, 61, 78, and 242%, respectively. Effects of the rat brain coil on amplitudes of static field and radiofrequency field uniformity were similar to each of the other coils. In vivo, whole-brain images of an adult male rat were acquired with a T(2)-weighted spin-echo sequence using an isotropic acquisition resolution of 0.25 x 0.25 x 0.25 mm(3) in 60.6 min. Multiplanar images of the in vivo rat brain with identification of anatomic structures are presented. Improvement in signal-to-noise ratio afforded by the rat brain coil may broaden experiments that utilize clinical MR scanners for in vivo image acquisition. 2010 Wiley-Liss, Inc.

Synthesis of coiled carbon nanotubes on Co/Al2O3 catalysts in a fluidised-bed

NASA Astrophysics Data System (ADS)

Liu, Jun; Harris, Andrew T.

2010-02-01

Mixtures of regularly coiled and straight multi-walled carbon nanotubes (MWNTs) were synthesised on alumina supported Co catalysts prepared by pH controlled, wet impregnation. The synthesis reaction was performed under C2H2:H2:N2 at 750 °C in a fluidised-bed for 30 min. Scanning electron microscopy/energy dispersive X-ray spectroscopy shows good distribution of the active Co particles on the surface of the alumina support. Determined from 10 individual SEM images from the same product batch, the CNTs present are typically from 10 to 40 nm in diameter. Thermogravimetric analysis (TGA) and Raman spectroscopy indicate the total oxidative weight loss is independent of pH during catalyst preparation. This study is the first to report the use of a fluidised-bed for the synthesis of coiled MWNTs, using alumina supported Co catalysts.

ELECTRICAL COIL STRUCTURE

DOEpatents

Baker, W.R.; Hartwig, A.

1962-09-25

A compactly wound electrical coil is designed for carrying intense pulsed currents such as are characteristic of controlled thermonuclear reaction devices. A flat strip of conductor is tightly wound in a spiral with a matching flat strip of insulator. To provide for a high fluid coolant flow through the coil with minimum pumping pressure, a surface of the conductor is scored with parallel transverse grooves which form short longitudinal coolant pasaages when the conductor is wound in the spiral configuration. Owing to this construction, the coil is extremely resistant to thermal and magnetic shock from sudden high currents. (AEC)

Structural Design and Thermal Analysis for Thermal Shields of the MICE Coupling Magnets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, Michael A.; Pan, Heng; Liu, X. K.

2009-07-01

A superconducting coupling magnet made from copper matrix NbTi conductors operating at 4 K will be used in the Muon Ionization Cooling Experiment (MICE) to produce up to 2.6 T on the magnet centerline to keep the muon beam within the thin RF cavity indows. The coupling magnet is to be cooled by two cryocoolers with a total cooling capacity of 3 W at 4.2 K. In order to keep a certain operating temperature margin, the most important is to reduce the heat leakage imposed on cold surfaces of coil cold mass assembly. An ntermediate temperature shield system placed betweenmore » the coupling coil and warm vacuum chamber is adopted. The shield system consists of upper neck shield, main shields, flexible connections and eight supports, which is to be cooled by the first stage cold heads of two ryocoolers with cooling capacity of 55 W at 60 K each. The maximum temperature difference on the shields should be less than 20 K, so the thermal analyses for the shields with different thicknesses, materials, flexible connections for shields' cooling and structure design for heir supports were carried out. 1100 Al is finally adopted and the maximum temperature difference is around 15 K with 4 mm shield thickness. The paper is to present detailed analyses on the shield system design.« less

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

PubMed Central

Bruhn, Jessica F.; Barnett, Katherine C.; Bibby, Jaclyn; Thomas, Jens M. H.; Keegan, Ronan M.; Rigden, Daniel J.; Bornholdt, Zachary A.

2014-01-01

The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle. PMID:24155387

Evaluating Stellarator Divertor Designs with EMC3

NASA Astrophysics Data System (ADS)

Bader, Aaron; Anderson, D. T.; Feng, Y.; Hegna, C. C.; Talmadge, J. N.

2013-10-01

In this paper various improvements of stellarator divertor design are explored. Next step stellarator devices require innovative divertor solutions to handle heat flux loads and impurity control. One avenue is to enhance magnetic flux expansion near strike points, somewhat akin to the X-Divertor concept in Tokamaks. The effect of judiciously placed external coils on flux deposition is calculated for configurations based on the HSX stellarator. In addition, we attempt to optimize divertor plate location to facilitate the external coil placement. Alternate areas of focus involve altering edge island size to elucidate the driving physics in the edge. The 3-D nature of stellarators complicates design and necessitates analysis of new divertor structures with appropriate simulation tools. We evaluate the various configurations with the coupled codes EMC3-EIRENE, allowing us to benchmark configurations based on target heat flux, impurity behavior, radiated power, and transitions to high recycling and detached regimes. Work supported by DOE-SC0006103.

Tx/Rx Head Coil Induces Less RF Transmit-Related Heating than Body Coil in Conductive Metallic Objects Outside the Active Area of the Head Coil

PubMed Central

Nagy, Zoltan; Oliver-Taylor, Aaron; Kuehne, Andre; Goluch, Sigrun; Weiskopf, Nikolaus

2017-01-01

The transmit–receive (Tx/Rx) birdcage head coil is often used for excitation instead of the body coil because of the presumably lower risk of heating in and around conductive implants. However, this common practice has not been systematically tested. To investigate whether the Tx/Rx birdcage head coil produces less heating than the body coil when scanning individuals with implants, we used a 3T clinical scanner and made temperature measurements around a straight 15 cm conductor using either the Tx/Rx body or the head coil for excitation. Additionally, the transmitted fields of a Tx/Rx head coil were measured both in air and in gel using a resonant and a non-resonant B field probes as well as a non-resonant E field probe. Simulations using a finite-difference time domain solver were compared with the experimental findings. When the body coil was used for excitation, we observed heating around the 15 cm wire at various anatomical locations (both within and outside of the active volume of the head coil). Outside its active area, no such heating was observed while using the Tx/Rx head coil for excitation. The E and B fields of the Tx/Rx birdcage head coil extended well-beyond the physical dimensions of the coil. In air, the fields were monotonically decreasing, while in gel they were more complex with local maxima at the end of the ASTM phantom. These experimental findings were line with the simulations. While caution must always be exercised when scanning individuals with metallic implants, these findings support the use of the Tx/Rx birdcage head coil in place of the body coil at 3T in order to reduce the risk of heating in and around conductive implants that are remote from the head coil. PMID:28184184

NMR insight into myosin-binding subunit coiled-coil structure reveals binding interface with protein kinase G-Iα leucine zipper in vascular function.

PubMed

Sharma, Alok K; Birrane, Gabriel; Anklin, Clemens; Rigby, Alan C; Alper, Seth L

2017-04-28

Nitrovasodilators relax vascular smooth-muscle cells in part by modulating the interaction of the C-terminal coiled-coil domain (CC) and/or the leucine zipper (LZ) domain of the myosin light-chain phosphatase component, myosin-binding subunit (MBS), with the N-terminal LZ domain of protein kinase G (PKG)-Iα. Despite the importance of vasodilation in cardiovascular homeostasis and therapy, our structural understanding of the MBS CC interaction with LZ PKG-1α has remained limited. Here, we report the 3D NMR solution structure of homodimeric CC MBS in which amino acids 932-967 form a coiled-coil of two monomeric α-helices in parallel orientation. We found that the structure is stabilized by non-covalent interactions, with dominant contributions from hydrophobic residues at a and d heptad positions. Using NMR chemical-shift perturbation (CSP) analysis, we identified a subset of hydrophobic and charged residues of CC MBS (localized within and adjacent to the C-terminal region) contributing to the dimer-dimer interaction interface between homodimeric CC MBS and homodimeric LZ PKG-Iα. 15 N backbone relaxation NMR revealed the dynamic features of the CC MBS interface residues identified by NMR CSP. Paramagnetic relaxation enhancement- and CSP-NMR-guided HADDOCK modeling of the dimer-dimer interface of the heterotetrameric complex exhibits the involvement of non-covalent intermolecular interactions that are localized within and adjacent to the C-terminal regions of each homodimer. These results deepen our understanding of the binding restraints of this CC MBS·LZ PKG-Iα low-affinity heterotetrameric complex and allow reevaluation of the role(s) of myosin light-chain phosphatase partner polypeptides in regulation of vascular smooth-muscle cell contractility. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Control of critical coupling in a coiled coaxial cable resonator.

PubMed

Huang, Jie; Wei, Tao; Wang, Tao; Fan, Jun; Xiao, Hai

2014-05-01

This paper reports a coiled coaxial cable resonator fabricated by cutting a slot in a spring-like coiled coaxial cable to produce a periodic perturbation. Electromagnetic coupling between two neighboring slots was observed. By manipulating the number of slots, critical coupling of the coiled coaxial cable resonator can be well controlled. An ultrahigh signal-to-noise ratio (over 50 dB) at the resonant frequency band was experimentally achieved from a coiled coaxial cable resonator with 38 turns. A theoretic model is developed to understand the device physics. The proposed device can be potentially used as a high quality and flexibly designed band-stop filter or a sensor in structural health monitoring.

Support Structure Design of the $$\\hbox{Nb}_{3}\\hbox{Sn}$$ Quadrupole for the High Luminosity LHC

DOE PAGES

Juchno, M.; Ambrosio, G.; Anerella, M.; ...

2014-10-31

New low-β quadrupole magnets are being developed within the scope of the High Luminosity LHC (HL-LHC) project in collaboration with the US LARP program. The aim of the HLLHC project is to study and implement machine upgrades necessary for increasing the luminosity of the LHC. The new quadrupoles, which are based on the Nb₃Sn superconducting technology, will be installed in the LHC Interaction Regions and will have to generate a gradient of 140 T/m in a coil aperture of 150 mm. In this paper, we describe the design of the short model magnet support structure and discuss results of themore » detailed 3D numerical analysis performed in preparation for the first short model test.« less

Structural Analysis of Hand Drawn Bumblebee Bombus terrestris Silk

PubMed Central

Woodhead, Andrea L.; Sutherland, Tara D.; Church, Jeffrey S.

2016-01-01

Bombus terrestris, commonly known as the buff-tailed bumblebee, is native to Europe, parts of Africa and Asia. It is commercially bred for use as a pollinator of greenhouse crops. Larvae pupate within a silken cocoon that they construct from proteins produced in modified salivary glands. The amino acid composition and protein structure of hand drawn B. terrestris, silk fibres was investigated through the use of micro-Raman spectroscopy. Spectra were obtained from single fibres drawn from the larvae salivary gland at a rate of 0.14 cm/s. Raman spectroscopy enabled the identification of poly(alanine), poly(alanine-glycine), phenylalanine, tryptophan, and methionine, which is consistent with the results of amino acid analysis. The dominant protein conformation was found to be coiled coil (73%) while the β-sheet content of 10% is, as expected, lower than those reported for hornets and ants. Polarized Raman spectra revealed that the coiled coils were highly aligned along the fibre axis while the β-sheet and random coil components had their peptide carbonyl groups roughly perpendicular to the fibre axis. The protein orientation distribution is compared to those of other natural and recombinant silks. A structural model for the B. terrestris silk fibre is proposed based on these results. PMID:27447623

Translocation of "rod-coil" polymers: probing the structure of single molecules within nanopores.

PubMed

de Haan, Hendrick W; Slater, Gary W

2013-01-25

Using simulation and analytical techniques, we demonstrate that it is possible to extract structural information about biological molecules by monitoring the dynamics as they translocate through nanopores. From Langevin dynamics simulations of polymers exhibiting discrete changes in flexibility (rod-coil polymers), distinct plateaus are observed in the progression towards complete translocation. Characterizing these dynamics via an incremental mean first passage approach, the large steps are shown to correspond to local barriers preventing the passage of the coils while the rods translocate relatively easily. Analytical replication of the results provides insight into the corrugated nature of the free energy landscape as well as the dependence of the effective barrier heights on the length of the coil sections. Narrowing the width of the pore or decreasing the charge on either the rod or the coil segments are both shown to enhance the resolution of structural details. The special case of a single rod confined within a nanopore is also studied. Here, sufficiently long flexible sections attached to either end are demonstrated to act as entropic anchors which can effectively trap the rod within the pore for an extended period of time. Both sets of results suggest new experimental approaches for the control and study of biological molecules within nanopores.

Numerical analysis of modified Central Solenoid insert design

DOE PAGES

Khodak, Andrei; Martovetsky, Nicolai; Smirnov, Aleksandre; ...

2015-06-21

The United States ITER Project Office (USIPO) is responsible for fabrication of the Central Solenoid (CS) for ITER project. The ITER machine is currently under construction by seven parties in Cadarache, France. The CS Insert (CSI) project should provide a verification of the conductor performance in relevant conditions of temperature, field, currents and mechanical strain. The US IPO designed the CSI that will be tested at the Central Solenoid Model Coil (CSMC) Test Facility at JAEA, Naka. To validate the modified design we performed three-dimensional numerical simulations using coupled solver for simultaneous structural, thermal and electromagnetic analysis. Thermal and electromagneticmore » simulations supported structural calculations providing necessary loads and strains. According to current analysis design of the modified coil satisfies ITER magnet structural design criteria for the following conditions: (1) room temperature, no current, (2) temperature 4K, no current, (3) temperature 4K, current 60 kA direct charge, and (4) temperature 4K, current 60 kA reverse charge. Fatigue life assessment analysis is performed for the alternating conditions of: temperature 4K, no current, and temperature 4K, current 45 kA direct charge. Results of fatigue analysis show that parts of the coil assembly can be qualified for up to 1 million cycles. Distributions of the Current Sharing Temperature (TCS) in the superconductor were obtained from numerical results using parameterization of the critical surface in the form similar to that proposed for ITER. Lastly, special ADPL scripts were developed for ANSYS allowing one-dimensional representation of TCS along the cable, as well as three-dimensional fields of TCS in superconductor material. Published by Elsevier B.V.« less

Endoluminal MR-guided ultrasonic applicator embedding cylindrical phased-array transducers and opposed-solenoid detection coil.

PubMed

Rata, Mihaela; Birlea, Vlad; Murillo, Adriana; Paquet, Christian; Cotton, François; Salomir, Rares

2015-01-01

MR-guided high-intensity contact ultrasound (HICU) was suggested as an alternative therapy for esophageal and rectal cancer. To offer high-quality MR guidance, two prototypes of receive-only opposed-solenoid coil were integrated with 64-element cylindrical phased-array ultrasound transducers (rectal/esophageal). The design of integrated coils took into account the transducer geometry (360° acoustic window within endoluminal space). The rectal coil was sealed on a plastic support and placed reversibly on the transducer head. The esophageal coil was fully embedded within the transducer head, resulting in one indivisible device. Comparison of integrated versus external coils was performed on a clinical 1.5T scanner. The integrated coils showed higher sensitivity compared with the standard extracorporeal coil with factors of up to 7.5 (rectal applicator) and 3.3 (esophageal applicator). High-resolution MR images for both anatomy (voxel 0.4 × 0.4 × 5 mm(3)) and thermometry (voxel 0.75 × 0.75 × 8 mm(3), 2 s/image) were acquired in vivo with the rectal endoscopic device. The temperature feedback loop accurately controlled multiple control points over the region of interest. This study showed significant improvement of MR data quality using endoluminal integrated coils versus standard external coil. Inframillimeter spatial resolution and accurate feedback control of MR-guided HICU thermotherapy were achieved. © 2014 Wiley Periodicals, Inc.

Comparison of the induced fields using different coil configurations during deep transcranial magnetic stimulation.

PubMed

Lu, Mai; Ueno, Shoogo

2017-01-01

Stimulation of deeper brain structures by transcranial magnetic stimulation (TMS) plays a role in the study of reward and motivation mechanisms, which may be beneficial in the treatment of several neurological and psychiatric disorders. However, electric field distributions induced in the brain by deep transcranial magnetic stimulation (dTMS) are still unknown. In this paper, the double cone coil, H-coil and Halo-circular assembly (HCA) coil which have been proposed for dTMS have been numerically designed. The distributions of magnetic flux density, induced electric field in an anatomically based realistic head model by applying the dTMS coils were numerically calculated by the impedance method. Results were compared with that of standard figure-of-eight (Fo8) coil. Simulation results show that double cone, H- and HCA coils have significantly deep field penetration compared to the conventional Fo8 coil, at the expense of induced higher and wider spread electrical fields in superficial cortical regions. Double cone and HCA coils have better ability to stimulate deep brain subregions compared to that of the H-coil. In the mean time, both double cone and HCA coils increase risk for optical nerve excitation. Our results suggest although the dTMS coils offer new tool with potential for both research and clinical applications for psychiatric and neurological disorders associated with dysfunctions of deep brain regions, the selection of the most suitable coil settings for a specific clinical application should be based on a balanced evaluation between stimulation depth and focality.

Optimization of 3D Field Design

NASA Astrophysics Data System (ADS)

Logan, Nikolas; Zhu, Caoxiang

2017-10-01

Recent progress in 3D tokamak modeling is now leveraged to create a conceptual design of new external 3D field coils for the DIII-D tokamak. Using the IPEC dominant mode as a target spectrum, the Finding Optimized Coils Using Space-curves (FOCUS) code optimizes the currents and 3D geometry of multiple coils to maximize the total set's resonant coupling. The optimized coils are individually distorted in space, creating toroidal ``arrays'' containing a variety of shapes that often wrap around a significant poloidal extent of the machine. The generalized perturbed equilibrium code (GPEC) is used to determine optimally efficient spectra for driving total, core, and edge neoclassical toroidal viscosity (NTV) torque and these too provide targets for the optimization of 3D coil designs. These conceptual designs represent a fundamentally new approach to 3D coil design for tokamaks targeting desired plasma physics phenomena. Optimized coil sets based on plasma response theory will be relevant to designs for future reactors or on any active machine. External coils, in particular, must be optimized for reliable and efficient fusion reactor designs. Work supported by the US Department of Energy under DE-AC02-09CH11466.

Degradation of the performance of an epoxy-impregnated REBCO solenoid due to electromagnetic forces

NASA Astrophysics Data System (ADS)

Matsuda, T.; Okamura, T.; Hamada, M.; Matsumoto, S.; Ueno, T.; Piao, R.; Yanagisawa, Y.; Maeda, H.

2018-03-01

Recently, degradation of a high-field REBCO coil due to strong electromagnetic forces, has been identified. This issue is related to a conductor movement, forming a kink in the conductor body, and hence epoxy impregnation should be effective to prevent it. The purpose of this paper is to examine the effect of epoxy impregnation on the electromagnetic force-induced degradation of a REBCO coil. We made an epoxy impregnated solenoid coil and charged it at 4.2 K in an external field of 11 T. A notable characteristic behavior, which is different from that of a dry or paraffin impregnated coil, was observed in the coil's performance. The coil did not show any normal voltage below 408 A, at 65% on the coil load line, but it showed a sudden voltage jump at 408 A, resulted from a sudden fracture of the REBCO conductor. The outward bending, combined with a strong circumferential stress, caused the REBCO layer to fracture. Although epoxy impregnation is effective to suppress a conductor movement inside the winding, avoiding self-supported sites at a coil edge is required to eliminate degradation of the thin and flexible REBCO conductor.

High frequency transformers and high Q factor inductors formed using epoxy-based magnetic polymer materials

DOEpatents

Sanchez, Robert O.; Gunewardena, Shelton; Masi, James V.

2007-11-27

An electrical component in the form of an inductor or transformer is disclosed which includes one or more coils and a magnetic polymer material located near the coils or supporting the coils to provide an electromagnetic interaction therewith. The magnetic polymer material is preferably a cured magnetic epoxy which includes a mercaptan derivative having a ferromagnetic atom chemically bonded therein. The ferromagnetic atom can be either a transition metal or rare-earth atom.

High frequency transformers and high Q factor inductors formed using epoxy-based magnetic polymer materials

DOEpatents

Sanchez, Robert O.; Gunewardena, Shelton; Masi, James V.

2005-03-29

An electrical component in the form of an inductor or transformer is disclosed which includes one or more coils and a magnetic polymer material located near the coils or supporting the coils to provide an electromagnetic interaction therewith. The magnetic polymer material is preferably a cured magnetic epoxy which includes a mercaptan derivative having a ferromagnetic atom chemically bonded therein. The ferromagnetic atom can be either a transition metal or rare-earth atom.

Monorail snare technique for the recovery of stretched platinum coils: technical case report.

PubMed

Fiorella, David; Albuquerque, Felipe C; Deshmukh, Vivek R; McDougall, Cameron G

2005-07-01

Coil stretching represents a potentially hazardous technical complication not infrequently encountered during the embolization of cerebral aneurysms. Often, the stretched coil cannot be advanced into the aneurysm or withdrawn intact. The operator is then forced to attempt to retract the damaged coil, which may result in coil breakage, leaving behind a significant length of potentially thrombogenic stretched coil material within the parent vessel. To overcome this problem, we devised a technique to snare the distal, unstretched, intact portion of the platinum coil by use of the indwelling microcatheter and stretched portion of the coil as a monorail guide. We have used this technique successfully in four patients to snare coils stretched during cerebral aneurysm embolization. Three of these patients were undergoing Neuroform (Boston Scientific/Target, Fremont, CA) stent-supported coil embolization of unruptured aneurysms. In all cases, the snare was advanced easily to the targeted site for coil engagement by use of the microcatheter as a monorail guide. Once the intact distal segment of the coil was ensnared, coil removal was uneventful, with no disturbance of the remainder of the indwelling coil pack or Neuroform stent. A 2-mm Amplatz Goose Neck microsnare (Microvena Corp., White Bear Lake, MN) was placed through a Prowler-14 microcatheter (Cordis Corp., Miami, FL). The hub of the indwelling SL-10 microcatheter (Boston Scientific, Natick, MA) was then cut away with a scalpel, leaving the coil pusher wire intact, and removed. The open 2-mm snare was then advanced over the outside of the coil pusher wire and microcatheter. The snare and Prowler-14 microcatheter were then advanced into the guiding catheter (6- or 7-French) as a unit over the indwelling SL-10 microcatheter. By use of the SL-10 microcatheter and coil as a "monorail" guide, the snare was advanced over and beyond the microcatheter and the stretched portion of the coil until the snare was in position to engage the distal unstretched coil. At this point, the snare was then closed around the intact portion of the coil, and the microcatheters, snare, and coil were removed as a unit. The monorail snare technique represents a fast, safe, and easy method by which a stretched coil can be removed.

Divertor Coil Design and Implementation on Pegasus

NASA Astrophysics Data System (ADS)

Shriwise, P. C.; Bongard, M. W.; Cole, J. A.; Fonck, R. J.; Kujak-Ford, B. A.; Lewicki, B. T.; Winz, G. R.

2012-10-01

An upgraded divertor coil system is being commissioned on the Pegasus Toroidal Experiment in conjunction with power system upgrades in order to achieve higher β plasmas, reduce impurities, and possibly achieve H-mode operation. Design points for the divertor coil locations and estimates of their necessary current ratings were found using predictive equilibrium modeling based upon a 300 kA target plasma. This modeling represented existing Pegasus coil locations and current drive limits. The resultant design calls for 125 kA-turns from the divertor system to support the creation of a double null magnetic topology in plasmas with Ip<=300 kA. Initial experiments using this system will employ 900 V IGBT power supply modules to provide IDIV<=4 kA. The resulting 20 kA-turn capability of the existing divertor coil will be augmented by a new coil providing additional A-turns in series. Induced vessel wall current modeling indicates the time response of a 28 turn augmentation coil remains fast compared to the poloidal field penetration rate through the vessel. First results operating the augmented system are shown.

Real-space transmission electron microscopy investigations of attachment of functionalized magnetic nanoparticles to DNA-coils acting as a biosensor.

PubMed

Akhtar, Sultan; Strömberg, Mattias; Zardán Gómez de la Torre, Teresa; Russell, Camilla; Gunnarsson, Klas; Nilsson, Mats; Svedlindh, Peter; Strømme, Maria; Leifer, Klaus

2010-10-21

The present work provides the first real-space analysis of nanobead-DNA coil interactions. Immobilization of oligonucleotide-functionalized magnetic nanobeads in rolling circle amplified DNA-coils was studied by complex magnetization measurements and transmission electron microscopy (TEM), and a statistical analysis of the number of beads hybridized to the DNA-coils was performed. The average number of beads per DNA-coil using the results from both methods was found to be around 6 and slightly above 2 for samples with 40 and 130 nm beads, respectively. The TEM analysis supported an earlier hypothesis that 40 nm beads are preferably immobilized in the interior of DNA-coils whereas 130 nm beads, to a larger extent, are immobilized closer to the exterior of the coils. The methodology demonstrated in the present work should open up new possibilities for characterization of interactions of a large variety of functionalized nanoparticles with macromolecules, useful for gaining more fundamental understanding of such interactions as well as for optimizing a number of biosensor applications.

Optimizing stellarator coil winding surfaces with Regcoil

NASA Astrophysics Data System (ADS)

Bader, Aaron; Landreman, Matt; Anderson, David; Hegna, Chris

2017-10-01

We show initial attempts at optimizing a coil winding surface using the Regcoil code [1] for selected quasi helically symmetric equilibria. We implement a generic optimization scheme which allows for variation of the winding surface to allow for improved diagnostic access and allow for flexible divertor solutions. Regcoil and similar coil-solving algorithms require a user-input winding surface, on which the coils lie. Simple winding surfaces created by uniformly expanding the plasma boundary may not be ideal. Engineering constraints on reactor design require a coil-plasma separation sufficient for the introduction of neutron shielding and a tritium generating blanket. This distance can be the limiting factor in determining reactor size. Furthermore, expanding coils in other regions, where possible, can be useful for diagnostic and maintenance access along with providing sufficient room for a divertor. We minimize a target function that includes as constraints, the minimum coil-plasma distance, the winding surface volume, and the normal magnetic field on the plasma boundary. Results are presented for two quasi-symmetric equilibria at different aspect ratios. Work supported by the US DOE under Grant DE-FG02-93ER54222.

Magnetic suspension and balance system advanced study

NASA Technical Reports Server (NTRS)

Boom, R. W.; Eyssa, Y. M.; Mcintosh, G. E.; Abdelsalam, M. K.

1985-01-01

An improved compact design for a superconducting magnetic suspension and balance system for an 8 ft. x 8 ft. transonic wind tunnel is developed. The original design of an MSBS in NASA Cr-3802 utilized 14 external superconductive coils and a superconductive solenoid in the airplane test model suspended in a wind tunnel. The improvements are in the following areas: test model solenoid options, dynamic force limits on the model, magnet cooling options, structure and cryogenic designs, power supply specifications, and cost and performance evaluations. The improvements are: MSBS cost reduction of 28%, weight; reduction of 43%, magnet system ampere-meter reduction of 38%, helium liquifier capacity reduction by 33%, magnet system stored energy reduction by 55%, AC loss to liquid helium reduced by 76%, system power supply reduced by 68%, test coil pole strength increased by 19%, wing magnetization increased by 40%, and control frequency limit increased by 200% from 10 Hz to 30 Hz. The improvements are due to: magnetic holmium coil forms in the test model, better rare earth permanent magnets in the wings, fiberglass-epoxy structure replacing stainless steel, better coil configuration, and new saddle roll coil design.

Optically tracked, single-coil, scanning magnetic induction tomography

NASA Astrophysics Data System (ADS)

Feldkamp, Joe R.; Quirk, Stephen

2017-03-01

Recent work has shown the feasibility of single-coil, magnetic induction tomography, for visualizing a 3D distribution of electrical conductivity in portions of the human body. Loss is measured in a single, planar coil consisting of concentric circular loops while the coil is relocated to various non-redundant positions and orientations in the vicinity of the target. These loss values, together with measured coil position and orientation, are processed by a quantitative mapping equation that enables reconstruction of an electrical conductivity image. Up until now, the position of the coil had to be established by a template, which required assignment of locations for the coil to visit without necessarily giving any prior consideration to target geometry. We have now added optical tracking to our existing single-coil device so that position and orientation are tracked automatically, allowing collection of coil loss data at arbitrary positions or orientations as needed. Optical tracking is accomplished via a set of IR reflective spheres mounted on the same enclosure that supports the coil. Position for a select sphere within the set, together with the four quaternions specifying optical body orientation, is fed to a laptop at the same time coil loss data is streamed to the same laptop via Bluetooth. The coil center can be tracked with sub-millimeter accuracy while orientation angle is known to a fraction of a degree. This work illustrates the use of single-coil MIT in full, position-orientation-tracked scan mode while imaging laboratory phantoms. Phantoms are based upon simple materials having biologic conductivity (< 5 S/m), including a cut of bone-in steak. The goal is not just to reconstruct an image that contains the features of the actual target, but also return correct conductivity values for the various features within the image.

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Haomin; Solberg, Jerome; Merzari, Elia

This paper describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLO formore » structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation« less

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

DOE PAGES

Yuan, Haomin; Solberg, Jerome; Merzari, Elia; ...

2017-08-01

This study describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980 s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLOmore » for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation.« less

Flow-induced vibration analysis of a helical coil steam generator experiment using large eddy simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Haomin; Solberg, Jerome; Merzari, Elia

This study describes a numerical study of flow-induced vibration in a helical coil steam generator experiment conducted at Argonne National Laboratory in the 1980 s. In the experiment, a half-scale sector model of a steam generator helical coil tube bank was subjected to still and flowing air and water, and the vibrational characteristics were recorded. The research detailed in this document utilizes the multi-physics simulation toolkit SHARP developed at Argonne National Laboratory, in cooperation with Lawrence Livermore National Laboratory, to simulate the experiment. SHARP uses the spectral element code Nek5000 for fluid dynamics analysis and the finite element code DIABLOmore » for structural analysis. The flow around the coil tubes is modeled in Nek5000 by using a large eddy simulation turbulence model. Transient pressure data on the tube surfaces is sampled and transferred to DIABLO for the structural simulation. The structural response is simulated in DIABLO via an implicit time-marching algorithm and a combination of continuum elements and structural shells. Tube vibration data (acceleration and frequency) are sampled and compared with the experimental data. Currently, only one-way coupling is used, which means that pressure loads from the fluid simulation are transferred to the structural simulation but the resulting structural displacements are not fed back to the fluid simulation.« less

Eddy Current Probe for Surface and Sub-Surface Inspection

NASA Technical Reports Server (NTRS)

Wincheski, Russell A. (Inventor); Simpson, John W. (Inventor)

2014-01-01

An eddy current probe includes an excitation coil for coupling to a low-frequency alternating current (AC) source. A magneto-resistive sensor is centrally disposed within and at one end of the excitation coil to thereby define a sensing end of the probe. A tubular flux-focusing lens is disposed between the excitation coil and the magneto-resistive sensor. An excitation wire is spaced apart from the magneto-resistive sensor in a plane that is perpendicular to the sensor's axis of sensitivity and such that, when the sensing end of the eddy current probe is positioned adjacent to the surface of a structure, the excitation wire is disposed between the magneto-resistive sensor and the surface of the structure. The excitation wire is coupled to a high-frequency AC source. The excitation coil and flux-focusing lens can be omitted when only surface inspection is required.

Structural domains required for channel function of the mouse transient receptor potential protein homologue TRP1beta.

PubMed

Engelke, Michael; Friedrich, Olaf; Budde, Petra; Schäfer, Christina; Niemann, Ursula; Zitt, Christof; Jüngling, Eberhard; Rocks, Oliver; Lückhoff, Andreas; Frey, Jürgen

2002-07-17

Transient receptor potential proteins (TRP) are supposed to participate in the formation of store-operated Ca(2+) influx channels by co-assembly. However, little is known which domains facilitate the interaction of subunits. Contribution of the N-terminal coiled-coil domain and ankyrin-like repeats and the putative pore region of the mouse TRP1beta (mTRP1beta) variant to the formation of functional cation channels were analyzed following overexpression in HEK293 (human embryonic kidney) cells. MTRP1beta expressing cells exhibited enhanced Ca(2+) influx and enhanced whole-cell membrane currents compared to mTRP1beta deletion mutants. Using a yeast two-hybrid assay only the coiled-coil domain facilitated homodimerization of the N-terminus. These results suggest that the N-terminus of mTRP1beta is required for structural organization thus forming functional channels.

Construction of a Chassis for a Tripartite Protein-Based Molecular Motor.

PubMed

Small, Lara S R; Bruning, Marc; Thomson, Andrew R; Boyle, Aimee L; Davies, Roberta B; Curmi, Paul M G; Forde, Nancy R; Linke, Heiner; Woolfson, Derek N; Bromley, Elizabeth H C

2017-06-16

Improving our understanding of biological motors, both to fully comprehend their activities in vital processes, and to exploit their impressive abilities for use in bionanotechnology, is highly desirable. One means of understanding these systems is through the production of synthetic molecular motors. We demonstrate the use of orthogonal coiled-coil dimers (including both parallel and antiparallel coiled coils) as a hub for linking other components of a previously described synthetic molecular motor, the Tumbleweed. We use circular dichroism, analytical ultracentrifugation, dynamic light scattering, and disulfide rearrangement studies to demonstrate the ability of this six-peptide set to form the structure designed for the Tumbleweed motor. The successful formation of a suitable hub structure is both a test of the transferability of design rules for protein folding as well as an important step in the production of a synthetic protein-based molecular motor.

Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.

PubMed

Koliopoulos, Marios G; Lethier, Mathilde; van der Veen, Annemarthe G; Haubrich, Kevin; Hennig, Janosch; Kowalinski, Eva; Stevens, Rebecca V; Martin, Stephen R; Reis E Sousa, Caetano; Cusack, Stephen; Rittinger, Katrin

2018-05-08

RIG-I is a viral RNA sensor that induces the production of type I interferon (IFN) in response to infection with a variety of viruses. Modification of RIG-I with K63-linked poly-ubiquitin chains, synthesised by TRIM25, is crucial for activation of the RIG-I/MAVS signalling pathway. TRIM25 activity is targeted by influenza A virus non-structural protein 1 (NS1) to suppress IFN production and prevent an efficient host immune response. Here we present structures of the human TRIM25 coiled-coil-PRYSPRY module and of complexes between the TRIM25 coiled-coil domain and NS1. These structures show that binding of NS1 interferes with the correct positioning of the PRYSPRY domain of TRIM25 required for substrate ubiquitination and provide a mechanistic explanation for how NS1 suppresses RIG-I ubiquitination and hence downstream signalling. In contrast, the formation of unanchored K63-linked poly-ubiquitin chains is unchanged by NS1 binding, indicating that RING dimerisation of TRIM25 is not affected by NS1.

Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111.

PubMed

Pulido, David; Hussain, Sadaf-Ahmahni; Hohenester, Erhard

2017-03-07

Laminins are cell-adhesive glycoproteins that are essential for basement membrane assembly and function. Integrins are important laminin receptors, but their binding site on the heterotrimeric laminins is poorly defined structurally. We report the crystal structure at 2.13 Å resolution of a minimal integrin-binding fragment of mouse laminin-111, consisting of ∼50 residues of α1β1γ1 coiled coil and the first three laminin G-like (LG) domains of the α1 chain. The LG domains adopt a triangular arrangement, with the C terminus of the coiled coil situated between LG1 and LG2. The critical integrin-binding glutamic acid residue in the γ1 chain tail is surface exposed and predicted to bind to the metal ion-dependent adhesion site in the integrin β1 subunit. Additional contacts to the integrin are likely to be made by the LG1 and LG2 surfaces adjacent to the γ1 chain tail, which are notably conserved and free of obstructing glycans. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Space-coiling fractal metamaterial with multi-bandgaps on subwavelength scale

NASA Astrophysics Data System (ADS)

Man, Xianfeng; Liu, Tingting; Xia, Baizhan; Luo, Zhen; Xie, Longxiang; Liu, Jian

2018-06-01

Acoustic metamaterials are remarkably different from conventional materials, as they can flexibly manipulate and control the propagation of sound waves. Unlike the locally resonant metamaterials introduced in earlier studies, we designed an ultraslow artificial structure with a sound speed much lower than that in air. In this paper, the space-coiling approach is proposed for achieving artificial metamaterial for extremely low-frequency airborne sound. In addition, the self-similar fractal technique is utilized for designing space-coiling Mie-resonance-based metamaterials (MRMMs) to obtain a band-dispersive spectrum. The band structures of two-dimensional (2D) acoustic metamaterials with different fractal levels are illustrated using the finite element method. The low-frequency bandgap can easily be formed, and multi-bandgap properties are observed in high-level fractals. Furthermore, the designed MRMMs with higher order fractal space coiling shows a good robustness against irregular arrangement. Besides, the proposed artificial structure was found to modify and control the radiation field arbitrarily. Thus, this work provides useful guidelines for the design of acoustic filtering devices and acoustic wavefront shaping applications on the subwavelength scale.

Design and testing of a coil-unit barrel for helical coil electromagnetic launcher

NASA Astrophysics Data System (ADS)

Yang, Dong; Liu, Zhenxiang; Shu, Ting; Yang, Lijia; Ouyang, Jianming

2018-01-01

A coil-unit barrel for a helical coil electromagnetic launcher is described. It provides better features of high structural strength and flexible adjustability. It is convenient to replace the damaged coil units and easy to adjust the number of turns in the stator coils due to the modular design. In our experiments, the highest velocity measured for a 4.5-kg projectile is 47.3 m/s and the mechanical reinforcement of the launcher could bear 35 kA peak current. The relationship between the energy conversion efficiency and the inductance gradient of the launcher is also studied. In the region of low inductance gradient, the efficiency is positively correlated with the inductance gradient. However, in the region of high inductance gradient, the inter-turn arc erosion becomes a major problem of limiting the efficiency and velocity of the launcher. This modular barrel allows further studies in the inter-turn arc and the variable inductance gradient helical coil launcher.

Design and testing of a coil-unit barrel for helical coil electromagnetic launcher.

PubMed

Yang, Dong; Liu, Zhenxiang; Shu, Ting; Yang, Lijia; Ouyang, Jianming

2018-01-01

A coil-unit barrel for a helical coil electromagnetic launcher is described. It provides better features of high structural strength and flexible adjustability. It is convenient to replace the damaged coil units and easy to adjust the number of turns in the stator coils due to the modular design. In our experiments, the highest velocity measured for a 4.5-kg projectile is 47.3 m/s and the mechanical reinforcement of the launcher could bear 35 kA peak current. The relationship between the energy conversion efficiency and the inductance gradient of the launcher is also studied. In the region of low inductance gradient, the efficiency is positively correlated with the inductance gradient. However, in the region of high inductance gradient, the inter-turn arc erosion becomes a major problem of limiting the efficiency and velocity of the launcher. This modular barrel allows further studies in the inter-turn arc and the variable inductance gradient helical coil launcher.

Mechanical properties and fibrin characteristics of endovascular coil–clot complexes: relevance to endovascular cerebral aneurysm repair paradigms

PubMed Central

Haworth, Kevin J; Weidner, Christopher R; Abruzzo, Todd A; Shearn, Jason T; Holland, Christy K

2015-01-01

Background Although coil embolization is known to prevent rebleeding from acutely ruptured cerebral aneurysms, the underlying biological and mechanical mechanisms have not been characterized. We sought to determine if microcoil-dependent interactions with thrombus induce structural and mechanical changes in the adjacent fibrin network. Such changes could play an important role in the prevention of aneurysm rebleeding. Methods The stiffness of in vitro human blood clots and coil–clot complexes implanted into aneurysm phantoms were measured immediately after formation and after retraction for 3 days using unconfined uniaxial compression assays. Scanning electron microscopy of the coil–clot complexes showed the effect of coiling on clot structure. Results The coil packing densities achieved were in the range of clinical practice. Bare platinum coils increased clot stiffness relative to clot alone (Young’s modulus 6.9 kPa and 0.83 kPa, respectively) but did not affect fibrin structure. Hydrogel-coated coils prevented formation of a clot and had no significant effect on clot stiffness (Young’s modulus 2 kPa) relative to clot alone. Clot age decreased fiber density by 0.2 fibers/µm2 but not the stiffness of the bare platinum coil–clot complex. Conclusions The stiffness of coil–clot complexes is related to the summative stiffness of the fibrin network and associated microcoils. Hydrogel-coated coils exhibit significantly less stiffness due to the mechanical properties of the hydrogel and the inhibition of fibrin network formation by the hydrogel. These findings have important implications for the design and engineering of aneurysm occlusion devices. PMID:24668257

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Manufacturing of REBCO coils strongly bonded to cooling members with epoxy resin aimed at its application to Maglev

NASA Astrophysics Data System (ADS)

Mizuno, Katsutoshi; Ogata, Masafumi; Hasegawa, Hitoshi

2014-11-01

The REBCO coated conductor has been attracted attention because of its high current density in the presence of high magnetic field. If the coated conductor is applied to Maglev, the operational temperature of the on-board magnets will be over 40 K and energy consumption of cryocoolers will be reduced. That high operational temperature also means the absence of liquid helium. Therefore, reliable thermal coupling is desirable for cooling the coils. We propose an epoxy impregnated REBCO coil co-wound with PTFE tape. While the PTFE tape prevents the performance degradation of the coil, the epoxy resin bonds the coil to cooling members. We carried out three experiments to confirm that the coil structure which we propose has robust thermal coupling without the degradation. First, thermal resistances of paraffin and epoxy were measured varying the temperature from room temperature to 10 K. The measurement result indicates that paraffin has a risk of losing thermal coupling during cooling down. In another experiment, PTFE (polytetrafluoroethylene) tape insulator prevented performance degradation of a small epoxy impregnated REBCO coil, while another REBCO coil with polyimide tape showed clear performance degradation. Finally, we produced a racetrack REBCO coil with the same outer dimension as a Maglev on-board magnet coil. Although the racetrack coil was installed in a GFRP coil case and tightly bonded to the case by epoxy impregnation, any performance degradation was not observed.

Solving coiled-coil protein structures

DOE PAGES

Dauter, Zbigniew

2015-02-26

With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.

Comparison of the induced fields using different coil configurations during deep transcranial magnetic stimulation

PubMed Central

Ueno, Shoogo

2017-01-01

Stimulation of deeper brain structures by transcranial magnetic stimulation (TMS) plays a role in the study of reward and motivation mechanisms, which may be beneficial in the treatment of several neurological and psychiatric disorders. However, electric field distributions induced in the brain by deep transcranial magnetic stimulation (dTMS) are still unknown. In this paper, the double cone coil, H-coil and Halo-circular assembly (HCA) coil which have been proposed for dTMS have been numerically designed. The distributions of magnetic flux density, induced electric field in an anatomically based realistic head model by applying the dTMS coils were numerically calculated by the impedance method. Results were compared with that of standard figure-of-eight (Fo8) coil. Simulation results show that double cone, H- and HCA coils have significantly deep field penetration compared to the conventional Fo8 coil, at the expense of induced higher and wider spread electrical fields in superficial cortical regions. Double cone and HCA coils have better ability to stimulate deep brain subregions compared to that of the H-coil. In the mean time, both double cone and HCA coils increase risk for optical nerve excitation. Our results suggest although the dTMS coils offer new tool with potential for both research and clinical applications for psychiatric and neurological disorders associated with dysfunctions of deep brain regions, the selection of the most suitable coil settings for a specific clinical application should be based on a balanced evaluation between stimulation depth and focality. PMID:28586349

Analysis of a flux-coupling type superconductor fault current limiter with pancake coils

NASA Astrophysics Data System (ADS)

Liu, Shizhuo; Xia, Dong; Zhang, Zhifeng; Qiu, Qingquan; Zhang, Guomin

2017-10-01

The characteristics of a flux-coupling type superconductor fault current limiter (SFCL) with pancake coils are investigated in this paper. The conventional double-wound non-inductive pancake coil used in AC power systems has an inevitable defect in Voltage Sourced Converter Based High Voltage DC (VSC-HVDC) power systems. Due to its special structure, flashover would occur easily during the fault in high voltage environment. Considering the shortcomings of conventional resistive SFCLs with non-inductive coils, a novel flux-coupling type SFCL with pancake coils is carried out. The module connections of pancake coils are performed. The electromagnetic field and force analysis of the module are contrasted under different parameters. To ensure proper operation of the module, the impedance of the module under representative operating conditions is calculated. Finally, the feasibility of the flux-coupling type SFCL in VSC-HVDC power systems is discussed.

Calculation of the Area of Stochastic Layer for a Single-Null Divertor Tokamak with the Effects of Dipole Coil Using Method of Maps

NASA Astrophysics Data System (ADS)

Basemore, Alphonso; Ali, Halima; Watson, Michael; Punjabi, Alkesh

1996-11-01

We calculate the variation in area of the stochastic scrape-off layer of a single-null divertor tokamak resulting from the effects of an externally placed dipole coil using the Method of Maps (Punjabi A, Verma A and Boozer A, Phys Rev Lett), 69, 3322 (1992) and J Plasma Phys, 52, 91 (1994). The unperturbed magnetic topology is represented by the Symmetric Simple Map (Ali H, Watson M, Mayer C, Punjabi A and Boozer A, Bull Am Phys Soc), 40, 1855 (1995). The effects of the dipole coil are repesented by the Dipole Map (Ali H, Watson M, Punjabi A and Boozer A, Sherwood Mtg), paper 1C20 (1996). A single dipole coil is placed across from the X-point below the last good surface. The strength of the dipole perturbation and the distance of the coil from last good surface are varied. The area of the stochastic layer is calculated using the method of fractal dimension. This work is supported by US DOE OFES. Alphonso Basemore is a HU CFRT Summer Fusion High School Workshop scholar from Mount Tabor High School in North Carolina. He is supported by NASA under its NASA SharpPlus Program.

Design study of steady-state 30-tesla liquid-neon-cooled magnet

NASA Technical Reports Server (NTRS)

Prok, G. M.; Brown, G. V.

1976-01-01

A design for a 30-tesla, liquid-neon-cooled magnet was reported which is capable of continuous operation. Cooled by nonboiling, forced-convection heat transfer to liquid neon flowing at 2.8 cu m/min in a closed, pressurized heat-transfer loop and structurally supported by a tapered structural ribbon, the tape-wound coils with a high-purity-aluminum conductor will produce over 30 teslas for 1 minute at 850 kilowatts. The magnet will have an inside diameter of 7.5 centimeters and an outside diameter of 54 centimeters. The minimum current density at design field will be 15.7 kA/sq cm.

Optimal Design of Litz Wire Coils With Sandwich Structure Wirelessly Powering an Artificial Anal Sphincter System.

PubMed

Ke, Lei; Yan, Guozheng; Yan, Sheng; Wang, Zhiwu; Li, Xiaoyang

2015-07-01

Transcutaneous energy transfer system (TETS) is widely used to energize implantable biomedical devices. As a key part of the TETS, a pair of applicable coils with low losses, high unloaded Q factor, and strong coupling is required to realize an efficient TETS. This article presents an optimal design methodology of planar litz wire coils sandwiched between two ferrite substrates wirelessly powering a novel mechanical artificial anal sphincter system for treating severe fecal incontinence, with focus on the main parameters of the coils such as the wire diameter, number of turns, geometry, and the properties of the ferrite substrate. The theoretical basis of optimal power transfer efficiency in an inductive link was analyzed. A set of analytical expressions are outlined to calculate the winding resistance of a litz wire coil on ferrite substrate, taking into account eddy-current losses, including conduction losses and induction losses. Expressions that describe the geometrical dimension dependence of self- and mutual inductance are derived. The influence of ferrite substrate relative permeability and dimensions is also considered. We have used this foundation to devise an applicable coil design method that starts with a set of realistic constraints and ends with the optimal coil pair geometries. All theoretical predictions are verified with measurements using different types of fabricated coils. The results indicate that the analysis is useful for optimizing the geometry design of windings and the ferrite substrate in a sandwich structure as part of which, in addition to providing design insight, allows speeding up the system efficiency-optimizing design process. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Robust SMES controller design for stabilization of inter-area oscillation considering coil size and system uncertainties

NASA Astrophysics Data System (ADS)

Ngamroo, Issarachai

2010-12-01

It is well known that the superconducting magnetic energy storage (SMES) is able to quickly exchange active and reactive power with the power system. The SMES is expected to be the smart storage device for power system stabilization. Although the stabilizing effect of SMES is significant, the SMES is quite costly. Particularly, the superconducting magnetic coil size which is the essence of the SMES, must be carefully selected. On the other hand, various generation and load changes, unpredictable network structure, etc., cause system uncertainties. The power controller of SMES which is designed without considering such uncertainties, may not tolerate and loses stabilizing effect. To overcome these problems, this paper proposes the new design of robust SMES controller taking coil size and system uncertainties into account. The structure of the active and reactive power controllers is the 1st-order lead-lag compensator. No need for the exact mathematical representation, system uncertainties are modeled by the inverse input multiplicative perturbation. Without the difficulty of the trade-off of damping performance and robustness, the optimization problem of control parameters is formulated. The particle swarm optimization is used for solving the optimal parameters at each coil size automatically. Based on the normalized integral square error index and the consideration of coil current constraint, the robust SMES with the smallest coil size which still provides the satisfactory stabilizing effect, can be achieved. Simulation studies in the two-area four-machine interconnected power system show the superior robustness of the proposed robust SMES with the smallest coil size under various operating conditions over the non-robust SMES with large coil size.

Design, Construction and Test of Cryogen-Free HTS Coil Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hocker, H.; Anerella, M.; Gupta, R.

2011-03-28

This paper will describe design, construction and test results of a cryo-mechanical structure to study coils made with the second generation High Temperature Superconductor (HTS) for the Facility for Rare Isotope Beams (FRIB). A magnet comprised of HTS coils mounted in a vacuum vessel and conduction-cooled with Gifford-McMahon cycle cryocoolers is used to develop and refine design and construction techniques. The study of these techniques and their effect on operations provides a better understanding of the use of cryogen free magnets in future accelerator projects. A cryogen-free, superconducting HTS magnet possesses certain operational advantages over cryogenically cooled, low temperature superconductingmore » magnets.« less

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

An Amino Acid Code for Irregular and Mixed Protein Packing

PubMed Central

Joo, Hyun; Chavan, Archana; Fraga, Keith; Tsai, Jerry

2015-01-01

To advance our understanding of protein tertiary structure, the development of the knob-socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob-socket model simplifies packing based on repeated patterns of 2 motifs: a 3 residue socket for packing within 2° structure and a 4 residue knob-socket for 3° packing. For coil and turn secondary structure, knob-sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α-helices to tertiary packing. Irregular secondary structure involves 3 residue cliques of consecutive contacting residues or XYZ sockets. In irregular sockets, Gly, Pro, Asp and Ser are favored, while Cys, His, Met and Trp are not. For irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly, while Cys, His, Met and Trp are not. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with an XYZ β-sheet socket may potentially function to inhibit β-sheet extension. In addition, analysis of the preferred crossing angles for strands within a β-sheet and mixed α-helices/β-sheets identifies canonical packing patterns useful in protein design. Lastly, the knob-socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map. PMID:26370334

Improved Separations of Proteins and Sugar Derivatives Using the Small-Scale Cross-Axis Coil Planet Centrifuge with Locular Multilayer Coiled Columns.

PubMed

Shinomiya, Kazufusa; Umezawa, Motoki; Seki, Manami; Nitta, Jun; Zaima, Kazumasa; Harikai, Naoki; Ito, Yoichiro

2016-12-01

Countercurrent chromatography (CCC) is liquid-liquid partition chromatography without using a solid support matrix. This technique requires further improvement of partition efficiency and shortening theseparation time. The locular multilayer coils modified with and without mixer glass beads were developed for the separation of proteins and 4-methylumbelliferyl (MU) sugar derivatives using the small-scale cross-axis coil planet centrifuge. Proteins were well separated from each other and the separation was improved at a low flow rate of the mobile phase. On the other hand, 4-MU sugar derivatives were sufficiently resolved with short separation time at a highflow rate of the mobile phase under satisfactory stationary phase retention. Effective separations were achieved using the locular multilayer coil for proteins with aqueous-aqueous polymer phase systems and for 4-MU sugar derivatives with organic-aqueous two-phase solvent systems by inserting a glass bead into each locule.

Plant tendrils: Nature's hygroscopic springs

NASA Astrophysics Data System (ADS)

Gerbode, Sharon; Puzey, Joshua; McCormick, Andrew; Mahadevan, L.

2012-02-01

Plant tendrils are specialized climbing organs that have fascinated biologists and physicists alike for centuries. Initially straight tendrils attach at the tip to an elevated rigid support and then winch the plant upward by coiling into a helical morphology characterized by two helices of opposite handedness connected by a helical perversion. In his renowned treatise on twining and tendril-bearing plants, Charles Darwin surmised that coiled tendrils serve as soft, springy attachments for the climbing plant. Yet, the true effect of the perverted helical shape of a coiled plant tendril has not been fully revealed. Using a combination of experiments on Cucurbitaceae tendrils, physical models constructed from strained rubber sheets, and numerical models of helical perversions, we have uncovered that tendril coiling occurs via anisotropic shrinkage of a strip of specialized cells in the interior of the tendril. Furthermore, variations in the mechanical behavior of tendrils as they become drier and ``woodier'' adds a new twist to the story of tendril coiling.

COLD TRAP

DOEpatents

Milleron, N.

1963-03-12

An improved linear-flow cold trap is designed for highvacuum applications such as mitigating back migration of diffusion pump oil moiecules. A central pot of liquid nitrogen is nested within and supported by a surrounding, vertical, helical coil of metai sheet, all enveloped by a larger, upright, cylindrical, vacuum vessel. The vertical interstices between successive turns of the coil afford lineal, axial, high-vacuum passages between open mouths at top and bottom of said vessel, while the coil, being cold by virtue of thermal contact of its innermost turn with the nitrogen pot, affords expansive proximate condensation surfaces. (AEC)

Amino Acid Substitutions of Coiled-Coil Protein Tpr Abrogate Anchorage to the Nuclear Pore Complex but Not Parallel, In-Register Homodimerization

PubMed Central

Hase, Manuela E.; Kuznetsov, Nikolai V.; Cordes, Volker C.

2001-01-01

Tpr is a protein component of nuclear pore complex (NPC)-attached intranuclear filaments. Secondary structure predictions suggest a bipartite structure, with a large N-terminal domain dominated by heptad repeats (HRs) typical for coiled-coil–forming proteins. Proposed functions for Tpr have included roles as a homo- or heteropolymeric architectural element of the nuclear interior. To gain insight into Tpr's ultrastructural properties, we have studied recombinant Tpr segments by circular dichroism spectroscopy, chemical cross-linking, and rotary shadowing electron microscopy. We show that polypeptides of the N-terminal domain homodimerize in vitro and represent α-helical molecules of extended rod-like shape. With the use of a yeast two-hybrid approach, arrangement of the coiled-coil is found to be in parallel and in register. To clarify whether Tpr can self-assemble further into homopolymeric filaments, the full-length protein and deletion mutants were overexpressed in human cells and then analyzed by confocal immunofluorescence microscopy, cell fractionation, and immuno-electron microscopy. Surplus Tpr, which does not bind to the NPC, remains in a soluble state of ∼7.5 S and occasionally forms aggregates of entangled molecules but neither self-assembles into extended linear filaments nor stably binds to other intranuclear structures. Binding to the NPC is shown to depend on the integrity of individual HRs; amino acid substitutions within these HRs abrogate NPC binding and render the protein soluble but do not abolish Tpr's general ability to homodimerize. Possible contributions of Tpr to the structural organization of the nuclear periphery in somatic cells are discussed. PMID:11514627

Near field wireless power transfer using curved relay resonators for extended transfer distance

NASA Astrophysics Data System (ADS)

Zhu, D.; Clare, L.; Stark, B. H.; Beeby, S. P.

2015-12-01

This paper investigates the performance of a near field wireless power transfer system that uses curved relay resonator to extend transfer distance. Near field wireless power transfer operates based on the near-field electromagnetic coupling of coils. Such a system can transfer energy over a relatively short distance which is of the same order of dimensions of the coupled coils. The energy transfer distance can be increased using flat relay resonators. Recent developments in printing electronics and e-textiles have seen increasing demand of embedding electronics into fabrics. Near field wireless power transfer is one of the most promising methods to power electronics on fabrics. The concept can be applied to body-worn textiles by, for example, integrating a transmitter coil into upholstery, and a flexible receiver coil into garments. Flexible textile coils take on the shape of the supporting materials such as garments, and therefore curved resonator and receiver coils are investigated in this work. Experimental results showed that using curved relay resonator can effectively extend the wireless power transfer distance. However, as the curvature of the coil increases, the performance of the wireless power transfer, especially the maximum received power, deteriorates.

An active magnetic bearing with high T(sub c) superconducting coils and ferromagnetic cores

NASA Technical Reports Server (NTRS)

Brown, G. V.; Dirusso, E.; Provenza, A. J.

1995-01-01

A proof-of-feasibility demonstration showed that high-T(sub c) superconductor (HTS) coils can be used in a high-load, active magnetic bearing in LN2. A homopolar radial bearing with commercially wound HTS (Bi 2223) bias and control coils produced over 890 N (200 lb) radial load capacity (measured non-rotatings) and supported a shaft to 14,000 rpm. The goal was to show that HTS coils can operate stably with ferromagnetic cores in a feedback controlled system at a current density similar to that for Cu in LN2. The bias coil, wound with non-twisted, multifilament HTS conductor, dissipated negligible power for its direct current. The control coils, wound with monofilament HTS sheathed in Ag, dissipated negligible power for direct current. AC losses increased rapidly with frequency and quadratically with AC amplitude. Above about 2 Hz, the effective resistance of the control coils exceeds that of the silver which is in electrical parallel with the oxide superconductor. These results show that twisted multifilament conductor is not needed for stable levitation but may be desired to reduce control power for sizable dynamic loads.

Active combustion flow modulation valve

DOEpatents

Hensel, John Peter; Black, Nathaniel; Thorton, Jimmy Dean; Vipperman, Jeffrey Stuart; Lambeth, David N; Clark, William W

2013-09-24

A flow modulation valve has a slidably translating hollow armature with at least one energizable coil wound around and fixably attached to the hollow armature. The energizable coil or coils are influenced by at least one permanent magnet surrounding the hollow armature and supported by an outer casing. Lorentz forces on the energizable coils which are translated to the hollow armature, increase or decrease the flow area to provide flow throttling action. The extent of hollow armature translation depends on the value of current supplied and the direction of translation depends on the direction of current flow. The compact nature of the flow modulation valve combined with the high forces afforded by the actuator design provide a flow modulation valve which is highly responsive to high-rate input control signals.

Membrane-spanning α-helical barrels as tractable protein-design targets.

PubMed

Niitsu, Ai; Heal, Jack W; Fauland, Kerstin; Thomson, Andrew R; Woolfson, Derek N

2017-08-05

The rational ( de novo ) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'. © 2017 The Author(s).

Induction magnetometer using a high-Tc superconductor coil

NASA Astrophysics Data System (ADS)

Sasada, Ichiro

2010-05-01

An induction magnetometer consisting of a search coil and an inverting operational amplifier is simple in structure and in signal transferring mechanism from the magnetic field input to the voltage output. Because this magnetometer is based on Faraday's law of induction, it has a lower cutoff frequency r/(2πL), where r is the resistance of the coil and L is its inductance. An attempt has been made to lower the cutoff frequency of the induction magnetometer by using a high-Tc superconductor coil. With a pancake coil (inner diameter ≈18 cm and outer diameter ≈23 cm, 92 turns, 3.23 mH) made of a Bismuth strontium calcium copper oxide (BSCCO) superconductor tape of 5 mm in width and 0.23 mm in thickness, the cutoff frequency achieved was 1.7 Hz which is much lower than that obtained with a bulky copper search coil which is typically in the range of 10-20 Hz. In the experiment, an inverting amplifier was made with a complementary metal-oxide semiconductor operational amplifier and was immersed in liquid nitrogen together with a BSCCO high-Tc superconducting coil. Discussion is made on the resolution of the induction magnetometer using a high-Tc superconductor search coil.

Multicoil resonance-based parallel array for smart wireless power delivery.

PubMed

Mirbozorgi, S A; Sawan, M; Gosselin, B

2013-01-01

This paper presents a novel resonance-based multicoil structure as a smart power surface to wirelessly power up apparatus like mobile, animal headstage, implanted devices, etc. The proposed powering system is based on a 4-coil resonance-based inductive link, the resonance coil of which is formed by an array of several paralleled coils as a smart power transmitter. The power transmitter employs simple circuit connections and includes only one power driver circuit per multicoil resonance-based array, which enables higher power transfer efficiency and power delivery to the load. The power transmitted by the driver circuit is proportional to the load seen by the individual coil in the array. Thus, the transmitted power scales with respect to the load of the electric/electronic system to power up, and does not divide equally over every parallel coils that form the array. Instead, only the loaded coils of the parallel array transmit significant part of total transmitted power to the receiver. Such adaptive behavior enables superior power, size and cost efficiency then other solutions since it does not need to use complex detection circuitry to find the location of the load. The performance of the proposed structure is verified by measurement results. Natural load detection and covering 4 times bigger area than conventional topologies with a power transfer efficiency of 55% are the novelties of presented paper.

Olfactomedin-1 Has a V-shaped Disulfide-linked Tetrameric Structure*

PubMed Central

Pronker, Matti F.; Bos, Trusanne G. A. A.; Sharp, Thomas H.; Thies-Weesie, Dominique M. E.; Janssen, Bert J. C.

2015-01-01

Olfactomedin-1 (Olfm1; also known as noelin and pancortin) is a member of the olfactomedin domain-containing superfamily and a highly expressed neuronal glycoprotein important for nervous system development. It binds a number of secreted proteins and cell surface-bound receptors to induce cell signaling processes. Using a combined approach of x-ray crystallography, solution scattering, analytical ultracentrifugation, and electron microscopy we determined that full-length Olfm1 forms disulfide-linked tetramers with a distinctive V-shaped architecture. The base of the “V” is formed by two disulfide-linked dimeric N-terminal domains. Each of the two V legs consists of a parallel dimeric disulfide-linked coiled coil with a C-terminal β-propeller dimer at the tips. This agrees with our crystal structure of a C-terminal coiled-coil segment and β-propeller combination (Olfm1coil-Olf) that reveals a disulfide-linked dimeric arrangement with the β-propeller top faces in an outward exposed orientation. Similar to its family member myocilin, Olfm1 is stabilized by calcium. The dimer-of-dimers architecture suggests a role for Olfm1 in clustering receptors to regulate signaling and sheds light on the conformation of several other olfactomedin domain family members. PMID:25903135

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Microtubule association of EML proteins and the EML4-ALK variant 3 oncoprotein require an N-terminal trimerization domain.

PubMed

Richards, Mark W; O'Regan, Laura; Roth, Daniel; Montgomery, Jessica M; Straube, Anne; Fry, Andrew M; Bayliss, Richard

2015-05-01

Proteins of the echinoderm microtubule (MT)-associated protein (EMAP)-like (EML) family contribute to formation of the mitotic spindle and interphase MT network. EML1-4 consist of Trp-Asp 40 (WD40) repeats and an N-terminal region containing a putative coiled-coil. Recurrent gene rearrangements in non-small cell lung cancer (NSCLC) fuse EML4 to anaplastic lymphoma kinase (ALK) causing expression of several oncogenic fusion variants. The fusions have constitutive ALK activity due to self-association through the EML4 coiled-coil. We have determined crystal structures of the coiled-coils from EML2 and EML4, which describe the structural basis of both EML self-association and oncogenic EML4-ALK activation. The structures reveal a trimeric oligomerization state directed by a conserved pattern of hydrophobic residues and salt bridges. We show that the trimerization domain (TD) of EML1 is necessary and sufficient for self-association. The TD is also essential for MT binding; however, this property requires an adjacent basic region. These observations prompted us to investigate MT association of EML4-ALK and EML1-ABL1 (Abelson 1) fusions in which variable portions of the EML component are present. Uniquely, EML4-ALK variant 3, which includes the TD and basic region of EML4 but none of the WD40 repeats, was localized to MTs, both when expressed recombinantly and when expressed in a patient-derived NSCLC cell line (H2228). This raises the question of whether the mislocalization of ALK activity to MTs might influence downstream signalling and malignant properties of cells. Furthermore, the structure of EML4 TD may enable the development of protein-protein interaction inhibitors targeting the trimerization interface, providing a possible avenue towards therapeutic intervention in EML4-ALK NSCLC.

Impact of magnetic field strength and receiver coil in ocular MRI: a phantom and patient study.

PubMed

Erb-Eigner, K; Warmuth, C; Taupitz, M; Willerding, G; Bertelmann, E; Asbach, P

2013-09-01

Generally, high-resolution MRI of the eye is performed with small loop surface coils. The purpose of this phantom and patient study was to investigate the influence of magnetic field strength and receiver coils on image quality in ocular MRI. The eyeball and the complex geometry of the facial bone were simulated by a skull phantom with swine eyes. MR images were acquired with two small loop surface coils with diameters of 4 cm and 7 cm and with a multi-channel head coil at 1.5 and 3 Tesla, respectively. Furthermore, MRI of the eye was performed prospectively in 20 patients at 1.5 Tesla (7 cm loop surface coil) and 3 Tesla (head coil). These images were analysed qualitatively and quantitatively and statistical significance was tested using the Wilcoxon-signed-rank test (a p-value of less than 0.05 was considered to indicate statistical significance). The analysis of the phantom images yielded the highest mean signal-to-noise ratio (SNR) at 3 Tesla with the use of the 4 cm loop surface coil. In the phantom experiment as well as in the patient studies the SNR was higher at 1.5 Tesla by applying the 7 cm surface coil than at 3 Tesla by applying the head coil. Concerning the delineation of anatomic structures no statistically significant differences were found. Our results show that the influence of small loop surface coils on image quality (expressed in SNR) in ocular MRI is higher than the influence of the magnetic field strength. The similar visibility of detailed anatomy leads to the conclusion that the image quality of ocular MRI at 3 Tesla remains acceptable by applying the head coil as a receiver coil. © Georg Thieme Verlag KG Stuttgart · New York.

The MaPLE device of Saha Institute of Nuclear Physics: construction and its plasma aspects.

PubMed

Pal, Rabindranath; Biswas, Subir; Basu, Subhasis; Chattopadhyay, Monobir; Basu, Debjyoti; Chaudhuri, Manis; Chowdhuri, Manis

2010-07-01

The Magnetized Plasma Linear Experimental (MaPLE) device is a low cost laboratory plasma device at Saha Institute of Nuclear Physics fabricated in-house with the primary aim of studying basic plasma physics phenomena such as plasma instabilities, wave propagation, and their nonlinear behavior in magnetized plasma regime in a controlled manner. The machine is specially designed to be a versatile laboratory device that can provide a number of magnetic and electric scenario to facilitate such studies. A total of 36 number of 20-turn magnet coils, designed such as to allow easy handling, is capable of producing a uniform, dc magnetic field of about 0.35 T inside the plasma chamber of diameter 0.30 m. Support structure of the coils is planned in an innovative way facilitating straightforward fabrication and easy positioning of the coils. Further special feature lies in the arrangement of the spacers between the coils that can be maneuvered rather easily to create different magnetic configurations. Various methods of plasma production can be suitably utilized according to the experimental needs at either end of the vacuum vessel. In the present paper, characteristics of a steady state plasma generated by electron cyclotron resonance method using 2.45 GHz microwave power are presented. Scans using simple probe drives revealed that a uniform and long plasma column having electron density approximately 3-5x10(10) cm(-3) and temperature approximately 7-10 eV, is formed in the center of the plasma chamber which is suitable for wave launching experiments.

Cryo-EM structure of the cytoplasmic domain of murine transient receptor potential cation channel subfamily C member 6 (TRPC6).

PubMed

Azumaya, Caleigh M; Sierra-Valdez, Francisco; Cordero-Morales, Julio F; Nakagawa, Terunaga

2018-05-11

The kidney maintains the internal milieu by regulating the retention and excretion of proteins, ions, and small molecules. The glomerular podocyte forms the slit diaphragm of the ultrafiltration filter, whose damage leads to progressive kidney failure and focal segmental glomerulosclerosis (FSGS). The canonical transient receptor potential 6 (TRPC6) ion channel is expressed in the podocyte and mutations in its cytoplasmic domain cause FSGS in humans. In vitro evaluation of disease-causing mutations in TRPC6 has revealed that these genetic alterations result in abnormal ion channel gating. However, the mechanism whereby the cytoplasmic domain modulates TRPC6 function is largely unknown. Here we report a cryoEM structure of the cytoplasmic domain of murine TRPC6 at 3.8Å resolution. The cytoplasmic fold of TRPC6 is characterized by an inverted dome-like chamber pierced by four radial horizontal helices that converge into a vertical coiled-coil at the central axis. Unlike in other TRP channels, TRPC6 displays a unique domain swap that occurs at the junction of the horizontal helices and coiled-coil. Multiple FSGS mutations converge at the buried interface between the vertical coiled-coil and the ankyrin repeats, which form the dome, suggesting these regions are critical for allosteric gating modulation. This functionally critical interface is a potential target for drug design. Importantly, dysfunction in other family members leads to learning deficits (TRPC1/4/5) and ataxia (TRPC3). Our data provide a structural framework for the mechanistic investigation of the TRPC family. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory.

PubMed

Chen, Mingchen; Zheng, Weihua; Wolynes, Peter G

2016-05-03

Aplysia cytoplasmic polyadenylation element binding (CPEB) protein, a translational regulator that recruits mRNAs and facilitates translation, has been shown to be a key component in the formation of long-term memory. Experimental data show that CPEB exists in at least a low-molecular weight coiled-coil oligomeric form and an amyloid fiber form involving the Q-rich domain (CPEB-Q). Using a coarse-grained energy landscape model, we predict the structures of the low-molecular weight oligomeric form and the dynamics of their transitions to the β-form. Up to the decamer, the oligomeric structures are predicted to be coiled coils. Free energy profiles confirm that the coiled coil is the most stable form for dimers and trimers. The structural transition from α to β is shown to be concentration dependent, with the transition barrier decreasing with increased concentration. We observe that a mechanical pulling force can facilitate the α-helix to β-sheet (α-to-β) transition by lowering the free energy barrier between the two forms. Interactome analysis of the CPEB protein suggests that its interactions with the cytoskeleton could provide the necessary mechanical force. We propose that, by exerting mechanical forces on CPEB oligomers, an active cytoskeleton can facilitate fiber formation. This mechanical catalysis makes possible a positive feedback loop that would help localize the formation of CPEB fibers to active synapse areas and mark those synapses for forming a long-term memory after the prion form is established. The functional role of the CPEB helical oligomers in this mechanism carries with it implications for targeting such species in neurodegenerative diseases.

Myocilin, a Component of a Membrane-Associated Protein Complex Driven by a Homologous Q-SNARE Domain

PubMed Central

Dismuke, W. Michael; McKay, Brian S.; Stamer, W. Daniel

2012-01-01

Myocilin is a widely expressed protein with no known function, however, mutations in myocilin appear to manifest uniquely as ocular hypertension and the blinding disease glaucoma. Using the protein homology/analogy recognition engine (PHYRE) we find that the olfactomedin domain of myocilin is similar in sequence motif and structure to a six-bladed, kelch repeat motif based on the known crystal structures of such proteins. Additionally, using sequence analysis we identify a coiled-coil segment of myocilin with homology to human Q-SNARE proteins. Using COS-7 cells expressing full length human myocilin and a version lacking the C-terminal olfactomedin domain, we identified a membrane-associated protein complex containing myocilin by hydrodynamic analysis. The myocilin construct that included the coiled-coil but lacked the olfactomedin domain formed complexes similar to the full-length protein, indicating that the coiled-coil domain of myocilin is sufficient for myocilin to bind to the large detergent resistant complex. In human retina and retinal pigment epithelium, which express myocilin, we detected the protein in a large, SDS-resistant, membrane-associated complex. We characterized the hydrodynamic properties of myocilin in human tissues as either a 15s complex with an Mr=405,000–440,000 yielding a slightly elongated globular shape similar to known SNARE complexes or a dimer of 6.4s and Mr=108,000. By identifying the Q-SNARE homology within the second coil of myocilin and documenting its participation in a SNARE-like complex, we provide evidence of a SNARE domain containing protein associated with a human disease. PMID:22463803

Volumetric wireless coil based on periodically coupled split-loop resonators for clinical wrist imaging.

PubMed

Shchelokova, Alena V; van den Berg, Cornelis A T; Dobrykh, Dmitry A; Glybovski, Stanislav B; Zubkov, Mikhail A; Brui, Ekaterina A; Dmitriev, Dmitry S; Kozachenko, Alexander V; Efimtcev, Alexander Y; Sokolov, Andrey V; Fokin, Vladimir A; Melchakova, Irina V; Belov, Pavel A

2018-02-09

Design and characterization of a new inductively driven wireless coil (WLC) for wrist imaging at 1.5 T with high homogeneity operating due to focusing the B 1 field of a birdcage body coil. The WLC design has been proposed based on a volumetric self-resonant periodic structure of inductively coupled split-loop resonators with structural capacitance. The WLC was optimized and studied regarding radiofrequency fields and interaction to the birdcage coil (BC) by electromagnetic simulations. The manufactured WLC was characterized by on-bench measurements and in vivo and phantom study in comparison to a standard cable-connected receive-only coil. The WLC placed into BC gave the measured B1+ increase of the latter by 8.6 times for the same accepted power. The phantom and in vivo wrist imaging showed that the BC in receiving with the WLC inside reached equal or higher signal-to-noise ratio than the conventional clinical setup comprising the transmit-only BC and a commercial receive-only flex-coil and created no artifacts. Simulations and on-bench measurements proved safety in terms of specific absorption rate and reflected transmit power. The results showed that the proposed WLC could be an alternative to standard cable-connected receive coils in clinical magnetic resonance imaging. As an example, with no cable connection, the WLC allowed wrist imaging on a 1.5 T clinical machine using a full-body BC for transmitting and receive with the desired signal-to-noise ratio, image quality, and safety. © 2018 International Society for Magnetic Resonance in Medicine.

Development and Comparison of Mechanical Structures for FNAL 15 T Nb$$_3$$Sn Dipole Demonstrator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novitski, I.; Zlobin, A. V.

2016-11-08

Main design challenges for 15 T accelerator magnets are large Lorentz forces at this field level. The large Lorentz forces generate high stresses in the coil and mechanical structure and, thus, need stress control to maintain them at the acceptable level for brittle Nb3Sn coils and other elements of magnet mechanical structure. To provide these conditions and achieve the design field in the FNAL 15 T dipole demonstrator, several mechanical structures have been developed and analysed. The possibilities and limitations of these designs are discussed in this paper

Demonstration of a stand-alone cylindrical fiber coil for optical amplifiers

NASA Astrophysics Data System (ADS)

Laxton, Steven R.; Bravo, Tyler; Madsen, Christi K.

2015-08-01

The design, fabrication and measurement of a cylindrical fiber coil structure is presented that has applications for compact fiber-optic amplifiers. A multimode fiber is used as a surrogate for a dual clad, rare-earth doped fiber for coil fabrication and optical testing. A ray trace algorithm, written in Python, was used to simulate the behavior of light travelling along the waveguide path. An in-house fabrication method was developed using 3D printed parts designed in SolidWorks and assembled with Arduino-controlled stepper motors for coil winding. Ultraviolet-cured epoxy was used to bind the coils into a rigid cylinder. Bend losses are introduced by the coil, and a measurement of the losses for two coil lengths was obtained experimentally. The measurements confirm that bend losses through a multimode fiber, representative of pump light propagating in a dual-clad rare-earth doped fiber, are relatively wavelength independent over a large spectral range and that higher order modes are extinguished quickly while lower order modes transmit through the windings with relatively low loss.

Cardiac cine imaging at 3 Tesla: initial experience with a 32-element body-array coil.

PubMed

Fenchel, Michael; Deshpande, Vibhas S; Nael, Kambiz; Finn, J Paul; Miller, Stephan; Ruehm, Stefan; Laub, Gerhard

2006-08-01

We sought to assess the feasibility of cardiac cine imaging and evaluate image quality at 3 T using a body-array coil with 32 coil elements. Eight healthy volunteers (3 men; median age 29 years) were examined on a 3-T magnetic resonance scanner (Magnetom Trio, Siemens Medical Solutions) using a 32-element phased-array coil (prototype from In vivo Corp.). Gradient-recalled-echo (GRE) cine (GRAPPAx3), GRE cine with tagging lines, steady-state-free-precession (SSFP) cine (GRAPPAx3 and x4), and SSFP cine(TSENSEx4 andx6) images were acquired in short-axis and 4-chamber view. Reference images with identical scan parameters were acquired using the total-imaging-matrix (Tim) coil system with a total of 12 coil elements. Images were assessed by 2 observers in a consensus reading with regard to image quality, noise and presence of artifacts. Furthermore, signal-to-noise values were determined in phantom measurements. In phantom measurements signal-to-noise values were increased by 115-155% for the various cine sequences using the 32-element coil. Scoring of image quality yielded statistically significant increased image quality with the SSFP-GRAPPAx4, SSFP-TSENSEx4, and SSFP-TSENSEx6 sequence using the 32-element coil (P < 0.05). Similarly, scoring of image noise yielded a statistically significant lower noise rating with the SSFP-GRAPPAx4, GRE-GRAPPAx3, SSFP-TSENSEx4, and SSFP-TSENSEx6 sequence using the 32-element coil (P < 0.05). This study shows that cardiac cine imaging at 3 T using a 32-element body-array coil is feasible in healthy volunteers. Using a large number of coil elements with a favorable sensitivity profile supports faster image acquisition, with high diagnostic image quality even for high parallel imaging factors.

System and method for storing energy

DOEpatents

Yarger, Eric Jay [Rigby, ID; Morrison, John [Butte, MT; Richardson, John Grant [Idaho Falls, ID; Spencer, David Frazer [Idaho Falls, ID; Christiansen, Dale W [Blackfoot, ID

2010-03-30

A self-recharging battery comprising a generator and an energy storage device contained within the battery case. The generator comprises a magnetic structure configured to generate a compressed magnetic field and a coil configured to focus the compressed magnetic field in electrical conductive elements of the coil.

Ultrastructural characterization of the tau-immunoreactive tubules in the oligodendroglial perikarya and their inner loop processes in progressive supranuclear palsy.

PubMed

Arima, K; Nakamura, M; Sunohara, N; Ogawa, M; Anno, M; Izumiyama, Y; Hirai, S; Ikeda, K

1997-06-01

Coiled bodies and interfascicular threads are conspicuous white matter abnormalities of brains of patients with progressive supranuclear palsy (PSP). Both structures are argyrophilic and immunoreactive for the microtubule-binding protein tau. This report concerns the ultrastructural localization of interfascicular threads and their relationship to coiled bodies in five PSP patients. We showed for the first time that abnormal tubules with a 13- to 15-nm diameter and fuzzy outer contours were the common structures of coiled bodies in the oligodendroglial perikarya and of interfascicular threads. Moreover, the tubules were immunolabeled by anti-tau antibodies. The abnormal tau-positive tubules of interfascicular threads were located in the inner loop of the myelin sheath. Our study further indicated that the thread-like structures in the white matter comprised, at least in part, oligodendroglial processes, and that they were also present in gray matter. We consider that the formation of coiled bodies in the perikarya and of interfascicular threads represents a common cytoskeletal abnormality of the oligodendroglia of PSP patients. Moreover, even though the white matter alterations of PSP resemble those of corticobasal degeneration, there are certain ultrastructural differences in the abnormal oligodendroglial tubules of the two diseases.

The structure of salt bridges between Arg(+) and Glu(-) in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries.

PubMed

Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

2015-06-07

Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu(-)) and arginine (Arg(+)) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu(-) and Arg(+), which provide a sensitive structural probe of Glu(-)⋯Arg(+) salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

The structure of salt bridges between Arg+ and Glu- in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries

NASA Astrophysics Data System (ADS)

Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R.; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

2015-06-01

Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu-) and arginine (Arg+) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu- and Arg+, which provide a sensitive structural probe of Glu-⋯Arg+ salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

Structural characterization of Mumps virus fusion protein core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Yueyong; Xu Yanhui; Lou Zhiyong

2006-09-29

The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus,more » forms typical 3-4-4-4-3 spacing. The similar charecterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.« less

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

NASA Astrophysics Data System (ADS)

Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte S.; Thomsen, Rasmus P.; Midtgaard, Søren Roi; Christensen, Niels Johan; Kjems, Jørgen; Thulstrup, Peter W.; Wengel, Jesper; Jensen, Knud J.

2016-07-01

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide-oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design.

Campaign for Levitation in LDX

NASA Astrophysics Data System (ADS)

Garnier, D. T.; Hansen, A. K.; Mauel, M. E.; Ortiz, E. E.; Boxer, A. C.; Ellsworth, J. L.; Karim, I.; Kesner, J.; Michael, P. C.; Zhukovsky, A.

2006-10-01

In the past year, preparations have been made for the first flight of the Levitated Dipole Experiment (LDX). LDX, which consists of a 560 kg superconducting coil floating within a 5 m diameter vacuum chamber, is designed to study fusion relevant plasmas confined in a dipole magnetic field. During the spring, a high temperature superconducting levitation coil was integrated into the LDX facility. Testing was undertaken to verify the thermal performance of the coil under expected levitation conditions. In addition, a real-time operating system digital control system was developed that will be used for the levitation control. In July, plasma experiments were conducted with all superconducting magnets in operation. While still supported, roughly 75% of the weight of the floating coil was magnetically lifted by the levitation coil above. A series of plasma experiments were conducted with the same magnetic geometry as will be the case during levitation. During August, the second generation launcher system will be installed. The launcher, which retracts beyond the plasma's last closed field lines during operation, is designed to safely catch the floating coil following an unexpected loss of control. After this installation, levitation experiments will commence.

Y stenting assisted coiling using a new low profile visible intraluminal support device for wide necked basilar tip aneurysms: a technical report.

PubMed

Conrad, Marcelo D; Brasiliense, Leonardo B C; Richie, Alexa N; Hanel, Ricardo A

2014-05-01

Many endovascular techniques have been described in recent years for the management of wide necked aneurysms. The Y stent assisted technique has been generally used for coil embolization of wide necked bifurcation aneurysms. This technique was first described for the treatment of basilar tip aneurysms in combination with several different devices, demonstrating encouraging results. We report the results of the first two cases of wide necked basilar tip aneurysms treated with Y stent assisted coil embolization using a new low profile visible intraluminal stent (LVIS Jr; MicroVention, Tustin, California, USA) delivered through a 0.017 inch microcatheter. We also reviewed the literature comparing other endovascular techniques (coiling alone, stent assisted coiling, and Y stent assisted coiling) for wide necked aneurysms. The LVIS Jr device offers a new option for the treatment of these challenging lesions, with clear advantages over currently available intracranial stents. Larger series and long term results are needed to confirm the applicability and durability of this technique/technology.

An asymmetric resonant coupling wireless power transmission link for Micro-Ball Endoscopy.

PubMed

Sun, Tianjia; Xie, Xiang; Li, Guolin; Gu, Yingke; Deng, Yangdong; Wang, Ziqiang; Wang, Zhihua

2010-01-01

This paper investigates the design and optimization of a wireless power transmission link targeting Micro-Ball Endoscopy applications. A novel asymmetric resonant coupling structure is proposed to deliver power to an endoscopic Micro-Ball system for image read-out after it is excreted. Such a technology enables many key medical applications with stringent requirements for small system volume and high power delivery efficiency. A prototyping power transmission sub-system of the Micro-Ball system was implemented. It consists of primary coil, middle resonant coil, and cube-like full-direction secondary receiving coils. Our experimental results proved that 200mW of power can be successfully delivered. Such a wireless power transmission capability could satisfy the requirements of the Micro-Ball based endoscopy application. The transmission efficiency is in the range of 41% (worst working condition) to 53% (best working condition). Comparing to conventional structures, Asymmetric Resonant Coupling Structure improves power efficiency by 13%.

Detection of Real Flaw using Uniform Eddy Current Multi-probe

NASA Astrophysics Data System (ADS)

Fukuoka, Katsuhiro; Hashimoto, Mitsuo

The establishment of the nondestructive inspection technology with plant structures has been stimulated by the recent occurrence of cracks in the nuclear power plant structures. In this research, a uniform eddy current multi-probe to apply to the complex structure and inspect the cracks at high-speed data acquisition was developed. Pick-up coils of the developed probe were arranged on a flexible printed circuit board. This probe was able to obtain clear signal for an EDM (electro-discharge machining) slit with 0.5 mm depth and distinguish EDM slits arranged at 2 mm intervals. It was confirmed that the SCC (stress corrosion cracking) of real flaw was able to be detected with developed uniform eddy current multi-probe by using the ferrite core for the exciting coil and considering the impedance matching of the exciting coil and the flaw detection device.

Catalytic reactor

DOEpatents

Aaron, Timothy Mark [East Amherst, NY; Shah, Minish Mahendra [East Amherst, NY; Jibb, Richard John [Amherst, NY

2009-03-10

A catalytic reactor is provided with one or more reaction zones each formed of set(s) of reaction tubes containing a catalyst to promote chemical reaction within a feed stream. The reaction tubes are of helical configuration and are arranged in a substantially coaxial relationship to form a coil-like structure. Heat exchangers and steam generators can be formed by similar tube arrangements. In such manner, the reaction zone(s) and hence, the reactor is compact and the pressure drop through components is minimized. The resultant compact form has improved heat transfer characteristics and is far easier to thermally insulate than prior art compact reactor designs. Various chemical reactions are contemplated within such coil-like structures such that as steam methane reforming followed by water-gas shift. The coil-like structures can be housed within annular chambers of a cylindrical housing that also provide flow paths for various heat exchange fluids to heat and cool components.

Magnetic field concentration using ferromagnetic material to propel a wireless power transfer based micro-robot

NASA Astrophysics Data System (ADS)

Kim, Dongwook; Park, Bumjin; Park, Jaehyoung; Park, Hyun Ho; Ahn, Seungyoung

2018-05-01

In this paper, we propose a novel coil structure, using a ferromagnetic material which concentrates the magnetic field, as the propulsion system of a wireless power transfer (WPT) based micro-robot. This structure uses an incident magnetic field to induce current during wireless power transfer, to generate a Lorentz force. To prevent net cancelation of the Lorentz force in the load coil, ferrite films were applied to one side of the coil segment. The demonstrated simplicity and effectiveness of the proposed micro-robot showed its suitability for applications. Simulation and experimental results confirmed a velocity of 1.02 mm/s with 6 mW power transfer capacity for the 3 mm sized micro-robot.

A Study of the Cold Resistance of Pipe Coiled Stock Produced at Foundry-Rolling Works. Part 2

NASA Astrophysics Data System (ADS)

Bagmet, O. A.; Naumenko, V. V.; Smetanin, K. S.

2018-03-01

Results of a study of coiled stock from low-carbon steels alloyed with manganese and silicon and different additives of niobium and titanium are presented. The coiled stock is produced at foundry-rolling works by the method of direct rolling of thin slabs right after their continuous casting. The microdeformation of the crystal lattice and the crystallographic texture are determined. The conditions of formation of the most favorable structure and texture in the steels are specified.

Dielectric properties of 3D-printed materials for anatomy specific 3D-printed MRI coils

NASA Astrophysics Data System (ADS)

Behzadnezhad, Bahareh; Collick, Bruce D.; Behdad, Nader; McMillan, Alan B.

2018-04-01

Additive manufacturing provides a low-cost and rapid means to translate 3D designs into the construction of a prototype. For MRI, this type of manufacturing can be used to construct various components including the structure of RF coils. In this paper, we characterize the material properties (dielectric constant and loss tangent) of several common 3D-printed polymers in the MRI frequency range of 63-300 MHz (for MRI magnetic field strengths of 1.5-7 T), and utilize these material properties in full-wave electromagnetic simulations to design and construct a very low-cost subject/anatomy-specific 3D-printed receive-only RF coil that fits close to the body. We show that the anatomy-specific coil exhibits higher signal-to-noise ratio compared to a conventional flat surface coil.

Optimization design of wireless charging system for autonomous robots based on magnetic resonance coupling

NASA Astrophysics Data System (ADS)

Wang, Junhua; Hu, Meilin; Cai, Changsong; Lin, Zhongzheng; Li, Liang; Fang, Zhijian

2018-05-01

Wireless charging is the key technology to realize real autonomy of mobile robots. As the core part of wireless power transfer system, coupling mechanism including coupling coils and compensation topology is analyzed and optimized through simulations, to achieve stable and practical wireless charging suitable for ordinary robots. Multi-layer coil structure, especially double-layer coil is explored and selected to greatly enhance coupling performance, while shape of ferrite shielding goes through distributed optimization to guarantee coil fault tolerance and cost effectiveness. On the basis of optimized coils, primary compensation topology is analyzed to adopt composite LCL compensation, to stabilize operations of the primary side under variations of mutual inductance. Experimental results show the optimized system does make sense for wireless charging application for robots based on magnetic resonance coupling, to realize long-term autonomy of robots.

Fourier transform-infrared spectroscopy as a diagnostic tool for mosquito coil smoke inhalation toxicity in Swiss Albino mice

NASA Astrophysics Data System (ADS)

Anusha, Chidambaram; Sankar, Renu; Varunkumar, Krishnamoorthy; Sivasindhuja, Gnanasambantham; Ravikumar, Vilwanathan

2017-12-01

The goal of this study is to establish Fourier transform-infrared (FTIR) spectroscopy as a diagnostic tool for allethrin-based mosquito coil smoke inhalation induced toxicity in mice. Primarily, we confirmed mosquito coil smoke inhalation toxicity in mice via reduced the body, organ weight and major vital organ tissue morphological structure changes. Furthermore, FTIR spectra was collected from control and mosquito coil smoke inhalation (8 h per day for 30 days) mice various tissues like liver, kidney, lung, heart and brain, to investigate the functional groups and their corresponding biochemical content variations. The FTIR spectra result shown major bio macromolecules such as protein and lipid functional peaks were shifted (decreased) in the mosquito coil smoke inhalation group as compared to control. The drastic peak shift was noticed in the liver, kidney followed by lung and brain. It is therefore concluded that the FTIR spectroscopy can be a successful detection tool in mosquito coil smoke inhalation toxicity.

A super-cusp divertor configuration for tokamaks

NASA Astrophysics Data System (ADS)

Ryutov, D. D.

2015-10-01

> This study demonstrates a remarkable flexibility of advanced divertor configurations created with the remote poloidal field coils. The emphasis here is on the configurations with three poloidal field nulls in the divertor area. We are seeking the structures where all three nulls lie on the same separatrix, thereby creating two zones of a very strong flux expansion, as envisaged in the concept of Takase's cusp divertor. It turns out that the set of remote coils can indeed produce a cusp divertor, with additional advantages of: (i) a large stand-off distance between the divertor and the coils and (ii) a thorough control that these coils exert over the fine features of the configuration. In reference to these additional favourable properties acquired by the cusp divertor, the resulting configuration could be called `a super-cusp'. General geometrical features of the three-null configurations produced by remote coils are described. Issues on the way to practical applications include the need for a more sophisticated control system and possible constraints related to excessively high currents in the divertor coils.

Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments.

PubMed

Gradišar, Helena; Božič, Sabina; Doles, Tibor; Vengust, Damjan; Hafner-Bratkovič, Iva; Mertelj, Alenka; Webb, Ben; Šali, Andrej; Klavžar, Sandi; Jerala, Roman

2013-06-01

Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

Biochemical and structural studies of the oligomerization domain of the Nipah virus phosphoprotein: evidence for an elongated coiled-coil homotrimer.

PubMed

Blocquel, David; Beltrandi, Matilde; Erales, Jenny; Barbier, Pascale; Longhi, Sonia

2013-11-01

Nipah virus (NiV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The NiV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the polymerase for transcription and replication. The polymerase is recruited onto the nucleocapsid via its cofactor, the phosphoprotein (P). The NiV P protein has a modular organization, with alternating disordered and ordered domains. Among these latter, is the P multimerization domain (PMD) that was predicted to adopt a coiled-coil conformation. Using both biochemical and biophysical approaches, we show that NiV PMD forms a highly stable and elongated coiled-coil trimer, a finding in striking contrast with respect to the PMDs of Paramyxoviridae members investigated so far that were all found to tetramerize. The present results therefore represent the first report of a paramyxoviral P protein forming trimers. © 2013 Elsevier Inc. All rights reserved.

Architecture and Flexibility of the Yeast Ndc80 Kinetochore Complex

PubMed Central

Wang, Hong-Wei; Long, Sydney; Ciferri, Claudio; Westermann, Stefan; Drubin, David; Barnes, Georjana; Nogales, Eva

2008-01-01

Kinetochores mediate microtubule–chromosome attachment and ensure accurate segregation of sister chromatids. The highly conserved Ndc80 kinetochore complex makes direct contacts with the microtubule and is essential for spindle checkpoint signaling. It contains a long coiled-coil region with globular domains at each end involved in kinetochore localization and microtubule binding, respectively. We have directly visualized the architecture of the yeast Ndc80 complex and found a dramatic kink within the 560-Å coiled-coil rod located about 160 Å from the larger globular head. Comparison of our electron microscopy images to the structure of the human Ndc80 complex allowed us to position the kink proximal to the microtubule-binding end and to define the conformational range of the complex. The position of the kink coincides with a coiled-coil breaking region conserved across eukaryotes. We hypothesize that the kink in Ndc80 is essential for correct kinetochore geometry and could be part of a tension-sensing mechanism at the kinetochore. PMID:18793650

Ereptiospiration.

PubMed

Woolley, Christine; Garcia, Antonio A; Santello, Marco

2017-04-12

Pure coconut oil, lanolin, and acetaminophen were vaporized at rates of 1-50 mg/min, using a porous network exhibiting a temperature gradient from 5000 to 5500 K/mm, without incurring noticeable chemical changes due to combustion, oxidation, or other thermally-induced chemical structural changes. The newly coined term "ereptiospiration" is used here to describe this combination of thermal transpiration at high temperature gradients since the process can force the creation of thermal aerosols by rapid heating in a localized zone. Experimental data were generated for these materials using two different supports for metering the materials to the battery powered coil: namely, a stainless steel fiber bundle and a 3-D printed steel cartridge. Heating coconut oil, lanolin, or acetaminophen in a beaker to lower temperatures than those achieved at the surface of the coil showed noticeable and rapid degradation in the samples, while visual and olfactory observations for ereptiospiration showed no noticeable degradation in lanolin and coconut oil while HPLC chromatograms along with visual observation confirm that within the limit of detection, acetaminophen remains chemically unaltered by ereptiospiration.

Crystallographic analysis of CD40 recognition and signaling by human TRAF2

PubMed Central

McWhirter, Sarah M.; Pullen, Steven S.; Holton, James M.; Crute, James J.; Kehry, Marilyn R.; Alber, Tom

1999-01-01

Tumor necrosis factor receptor superfamily members convey signals that promote diverse cellular responses. Receptor trimerization by extracellular ligands initiates signaling by recruiting members of the tumor necrosis factor receptor-associated factor (TRAF) family of adapter proteins to the receptor cytoplasmic domains. We report the 2.4-Å crystal structure of a 22-kDa, receptor-binding fragment of TRAF2 complexed with a functionally defined peptide from the cytoplasmic domain of the CD40 receptor. TRAF2 forms a mushroom-shaped trimer consisting of a coiled coil and a unique β-sandwich domain. Both domains mediate trimerization. The CD40 peptide binds in an extended conformation with every side chain in contact with a complementary groove on the rim of each TRAF monomer. The spacing between the CD40 binding sites on TRAF2 supports an elegant signaling mechanism in which trimeric, extracellular ligands preorganize the receptors to simultaneously recognize three sites on the TRAF trimer. PMID:10411888

A Figure-of-Merit for Designing High-Performance Inductive Power Transmission Links

PubMed Central

Kiani, Mehdi; Ghovanloo, Maysam

2014-01-01

Power transfer efficiency (PTE) and power delivered to the load (PDL) are two key inductive link design parameters that relate to the power source and driver specs, power loss, transmission range, robustness against misalignment, variations in loading, and interference with other devices. Designers need to strike a delicate balance between these two because designing the link to achieve high PTE will degrade the PDL and vice versa. We are proposing a new figure-of-merit (FoM), which can help designers to find out whether a two-, three-, or four-coil link is appropriate for their particular application and guide them through an iterative design procedure to reach optimal coil geometries based on how they weigh the PTE versus PDL for that application. Three design examples at three different power levels have been presented based on the proposed FoM for implantable microelectronic devices, handheld mobile devices, and electric vehicles. The new FoM suggests that the two-coil links are suitable when the coils are strongly coupled, and a large PDL is needed. Three-coil links are the best when the coils are loosely coupled, the coupling distance varies considerably, and large PDL is necessary. Finally, four-coil links are optimal when the PTE is paramount, the coils are loosely coupled, and their relative distance and alignment are stable. Measurement results support the accuracy of the theoretical design procedure and conclusions. PMID:25382898

A Figure-of-Merit for Designing High-Performance Inductive Power Transmission Links.

PubMed

Kiani, Mehdi; Ghovanloo, Maysam

2012-11-16

Power transfer efficiency (PTE) and power delivered to the load (PDL) are two key inductive link design parameters that relate to the power source and driver specs, power loss, transmission range, robustness against misalignment, variations in loading, and interference with other devices. Designers need to strike a delicate balance between these two because designing the link to achieve high PTE will degrade the PDL and vice versa. We are proposing a new figure-of-merit (FoM), which can help designers to find out whether a two-, three-, or four-coil link is appropriate for their particular application and guide them through an iterative design procedure to reach optimal coil geometries based on how they weigh the PTE versus PDL for that application. Three design examples at three different power levels have been presented based on the proposed FoM for implantable microelectronic devices, handheld mobile devices, and electric vehicles. The new FoM suggests that the two-coil links are suitable when the coils are strongly coupled, and a large PDL is needed. Three-coil links are the best when the coils are loosely coupled, the coupling distance varies considerably, and large PDL is necessary. Finally, four-coil links are optimal when the PTE is paramount, the coils are loosely coupled, and their relative distance and alignment are stable. Measurement results support the accuracy of the theoretical design procedure and conclusions.

Single-coil and dual-coil defibrillator leads and association with clinical outcomes in a complete Danish nationwide ICD cohort.

PubMed

Larsen, Jacob M; Hjortshøj, Søren P; Nielsen, Jens C; Johansen, Jens B; Petersen, Helen H; Haarbo, Jens; Johansen, Martin B; Thøgersen, Anna Margrethe

2016-03-01

The best choice of defibrillator lead in patients with routine implantable cardioverter-defibrillator (ICD) is not settled. Traditionally, most physicians prefer dual-coil leads but the use of single-coil leads is increasing. The purpose of this study was to compare clinical outcomes in patients with single- and dual-coil leads. All 4769 Danish patients 18 years or older with first-time ICD implants from 2007 to 2011 were included from the Danish Pacemaker and ICD Register. Defibrillator leads were 38.9% single-coil leads and 61.1% dual-coil leads. The primary end point was all-cause mortality. Secondary end points were lowest successful energy at implant defibrillation testing, first shock failure in spontaneous arrhythmias, structural lead failure, and lead extraction outcomes. Single-coil leads were associated with lower all-cause mortality with an adjusted hazard ratio of 0.85 (95% confidence interval 0.73-0.99; P = .04). This finding was robust in a supplementary propensity score-matched analysis. However, dual-coil leads were used in patients with slightly higher preimplant morbidity, making residual confounding by indication the most likely explanation for the observed association between lead type and mortality. The lowest successful defibrillation energy was higher using single-coil leads (23.2 ± 4.3 J vs 22.1 ± 3.9 J; P < .001). No significant differences were observed for other secondary end points showing high shock efficacies and low rates of lead failures and extraction complications. Shock efficacy is high for modern ICD systems. The choice between single-coil and dual-coil defibrillator leads is unlikely to have a clinically significant impact on patient outcomes in routine ICD implants. Copyright © 2016 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

High-Temperature, High-Load-Capacity Radial Magnetic Bearing

NASA Technical Reports Server (NTRS)

Provenza, Andrew; Montague, Gerald; Kascak, Albert; Palazzolo, Alan; Jansen, Ralph; Jansen, Mark; Ebihara, Ben

2005-01-01

A radial heteropolar magnetic bearing capable of operating at a temperature as high as 1,000 F (=540 C) has been developed. This is a prototype of bearings for use in gas turbine engines operating at temperatures and speeds much higher than can be withstood by lubricated rolling-element bearings. It is possible to increase the maximum allowable operating temperatures and speeds of rolling-element bearings by use of cooling-air systems, sophisticated lubrication systems, and rotor-vibration- damping systems that are subsystems of the lubrication systems, but such systems and subsystems are troublesome. In contrast, a properly designed radial magnetic bearing can suspend a rotor without contact, and, hence, without need for lubrication or for cooling. Moreover, a magnetic bearing eliminates the need for a separate damping system, inasmuch as a damping function is typically an integral part of the design of the control system of a magnetic bearing. The present high-temperature radial heteropolar magnetic bearing has a unique combination of four features that contribute to its suitability for the intended application: 1. The wires in its electromagnet coils are covered with an insulating material that does not undergo dielectric breakdown at high temperature and is pliable enough to enable the winding of the wires to small radii. 2. The processes used in winding and potting of the coils yields a packing factor close to 0.7 . a relatively high value that helps in maximizing the magnetic fields generated by the coils for a given supplied current. These processes also make the coils structurally robust. 3. The electromagnets are of a modular C-core design that enables replacement of components and semiautomated winding of coils. 4. The stator is mounted in such a manner as to provide stable support under radial and axial thermal expansion and under a load as large as 1,000 lb (.4.4 kN).

Axial flow plasma shutter

DOEpatents

Krausse, George J.

1988-01-01

A shutter (36) is provided for controlling a beam, or current, of charged particles in a device such as a thyratron (10). The substrate (38) defines an aperture (60) with a gap (32) which is placeable within the current. Coils (48) are formed on the substrate (38) adjacent the aperture (60) to produce a magnetic field for trapping the charged particles in or about aperture (60). The proximity of the coils (48) to the aperture (60) enables an effective magnetic field to be generated by coils (48) having a low inductance suitable for high frequency control. The substantially monolithic structure including the substrate (38) and coils (48) enables the entire shutter assembly (36) to be effectively located with respect to the particle beam.

Development of a Tunnel Diode Resonator technique for magnetic measurements in Electrostatic Levitation chamber

NASA Astrophysics Data System (ADS)

Spyrison, N. S.; Prommapan, P.; Kim, H.; Maloney, J.; Rustan, G. E.; Kreyssig, A.; Goldman, A. I.; Prozorov, R.

2011-03-01

The incorporation of the Tunnel Diode Resonator (TDR) technique into an ElectroStatic Levitation (ESL) apparatus was explored. The TDR technique is known to operate and behave well at low temperatures with careful attention to coil-sample positioning in a dark, shielded environment. With these specifications a frequency resolution of 10-9 in a few seconds counting time can be achieved. Complications arise when this technique is applied in the ESL chamber where a sample of molten metal is levitating less then 10 mm from the coil in a large electrostatic field. We have tested a variety of coils unconventional to TDR; including Helmholtz pairs and Archimedean spiral coils. Work was supported by the Nation Science Foundation under grant DMR-08-17157

Some Aspects of an Air-Core Single-Coil Magnetic Suspension System

NASA Technical Reports Server (NTRS)

Hamlet, Irvin L.; Kilgore, Robert A.

1966-01-01

This paper presents some of the technical aspects in the development at the Langley Research Center of an air-cove, dual-wound, single-coil, magnetic-suspension system with one-dimensional control. Overall electrical system design features and techniques are discussed in addition to the problems of control and stability. Special treatment is given to the operation of a dual-wound, high-current support coil which provides the bias fields and superimposed modulated field. Other designs features include a six-phase, solid-state power stage for modulation of the relatively large magnitude control current, and an associated six-phase trigger circuit.

Design of beta-domain swapping, alpha/beta-protein, environmentally sensitive coiled coil and peptide functionalized titania materials

NASA Astrophysics Data System (ADS)

Nagarkar, Radhika P.

2009-12-01

The objective of this dissertation is to apply rational peptide design to fabricate nanomaterials via self-assembly. This has been demonstrated in structurally diverse systems with an aim of deciphering the underlying principles governing how sequence affects the peptide's ability to adopt a specific secondary structure and ultimate material properties that are realized from the association of these secondary structural elements. Several amyloidogenic proteins have been shown to self-assemble into fibrils using a mechanism known as domain swapping. Here, discreet units of secondary structure are exchanged among discreet proteins during self-assembly to form extended networks with precise three dimensional organization. The possibility of using these mechanisms to design peptides capable of controlled assembly and fibril formation leading to materials with targeted properties is explored. By altering the placement of a beta-turn sequence that varies the size and location of the exchanged strand, twisting, non-twisting and laminated fibrillar nanostructures are obtained. Hydrogels prepared from these strand swapping beta-hairpins have varied rheological properties due to differences in their fibrillar nanostructures. In a second distinct design, alpha/beta-proteins are used to prepare environmentally sensitive hydrogels. Here, multiple distinct motifs for structural integrity and dynamic response within a single self-assembling peptide allow the amyloid-like fibrils formed to controllably alter their nano-topography in response to an external stimulus such as temperature. The development of these self-assembling alpha/beta-protein motifs also necessitated the design of pH sensitive antiparallel coiled coils. Exploring the basic principles responsible for pH dependent conformational changes in coiled coils can lead to new insights in the control of protein structure and function. Lastly, this dissertation discusses the interface between biomolecules and inorganic materials. Here, a new methodology of functionalizing titania nanoparticles with peptides is developed. In all of these different material forming systems, extensive biophysical characterization by circular dichroism spectroscopy, fourier transform infrared spectroscopy, X-ray diffraction and analytical ultracentrifugation is performed to understand peptide folding and self-assembly. Careful nanostructural characterization by electron and force microscopies is performed to elucidate self-assembly mechanisms and has proved to be vital in applying the iterative design process to develop responsive nanomaterials.

Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization

NASA Astrophysics Data System (ADS)

Elkin, Carl D.; Zuccola, Harmon J.; Hogle, James M.; Joseph-McCarthy, Diane

2000-11-01

Hepatitis delta virus (HDV) encodes a single polypeptide called hepatitis delta antigen (DAg). Dimerization of DAg is required for viral replication. The structure of the dimerization region, residues 12 to 60, consists of an anti-parallel coiled coil [Zuccola et al., Structure, 6 (1998) 821]. Multiple Copy Simultaneous Searches (MCSS) of the hydrophobic core region formed by the bend in the helix of one monomer of this structure were carried out for many diverse functional groups. Six critical interaction sites were identified. The Protein Data Bank was searched for backbone templates to use in the subsequent design process by matching to these sites. A 14 residue helix expected to bind to the d-isomer of the target structure was selected as the template. Over 200 000 mutant sequences of this peptide were generated based on the MCSS results. A secondary structure prediction algorithm was used to screen all sequences, and in general only those that were predicted to be highly helical were retained. Approximately 100 of these 14-mers were model built as d-peptides and docked with the l-isomer of the target monomer. Based on calculated interaction energies, predicted helicity, and intrahelical salt bridge patterns, a small number of peptides were selected as the most promising candidates. The ligand design approach presented here is the computational analogue of mirror image phage display. The results have been used to characterize the interactions responsible for formation of this model anti-parallel coiled coil and to suggest potential ligands to disrupt it.

Exploring the potential of a multi-level approach to improve capability for continuous organizational improvement and learning in a Swedish healthcare region.

PubMed

Nyström, M E; Höög, E; Garvare, R; Andersson Bäck, M; Terris, D D; Hansson, J

2018-05-24

Eldercare and care of people with functional impairments is organized by the municipalities in Sweden. Improving care in these areas is complex, with multiple stakeholders and organizations. Appropriate strategies to develop capability for continuing organizational improvement and learning (COIL) are needed. The purpose of our study was to develop and pilot-test a flexible, multilevel approach for COIL capability building and to identify what it takes to achieve changes in key actors' approaches to COIL. The approach, named "Sustainable Improvement and Development through Strategic and Systematic Approaches" (SIDSSA), was applied through an action-research and action-learning intervention. The SIDSSA approach was tested in a regional research and development (R&D) unit, and in two municipalities handling care of the elderly and people with functional impairments. Our approach included a multilevel strategy, development loops of five flexible phases, and an action-learning loop. The approach was designed to support systems understanding, strategic focus, methodological practices, and change process knowledge - all of which required double-loop learning. Multiple qualitative methods, i.e., repeated interviews, process diaries, and documents, provided data for conventional content analyses. The new approach was successfully tested on all cases and adopted and sustained by the R&D unit. Participants reported new insights and skills. The development loop facilitated a sense of coherence and control during uncertainty, improved planning and problem analysis, enhanced mapping of context and conditions, and supported problem-solving at both the individual and unit levels. The systems-level view and structured approach helped participants to explain, motivate, and implement change initiatives, especially after working more systematically with mapping, analyses, and goal setting. An easily understood and generalizable model internalized by key organizational actors is an important step before more complex development models can be implemented. SIDSSA facilitated individual and group learning through action-learning and supported systems-level views and structured approaches across multiple organizational levels. Active involvement of diverse organizational functions and levels in the learning process was facilitated. However, the time frame was too short to fully test all aspects of the approach, specifically in reaching beyond the involved managers to front-line staff and patients.

Mitochondrial CHCHD-Containing Proteins: Physiologic Functions and Link with Neurodegenerative Diseases.

PubMed

Zhou, Zhi-Dong; Saw, Wuan-Ting; Tan, Eng-King

2017-09-01

The coiled-coil-helix-coiled-coil-helix domain (CHCHD)-containing proteins are evolutionarily conserved nucleus-encoded small mitochondrial proteins with important functions. So far, nine members have been identified in this protein family. All CHCHD proteins have at least one functional coiled-coil-helix-coiled-coil-helix (CHCH) domain, which is stabilized by two pairs of disulfide bonds between two helices. CHCHD proteins have various important pathophysiological roles in mitochondria and other key cellular processes. Mutations of CHCHD proteins have been associated with various human neurodegenerative diseases. Mutations of CHCHD10 are associated with amyotrophic lateral sclerosis (ALS) and/or frontotemporal lobe dementia (FTD), motor neuron disease, and late-onset spinal muscular atrophy and autosomal dominant mitochondrial myopathy. CHCHD10 stabilizes mitochondrial crista ultrastructure and maintains its integrity. In patients with CHCHD10 mutations, there are abnormal mitochondrial crista structure, deficiencies of respiratory chain complexes, impaired mitochondrial respiration, and multiple mitochondrial DNA (mtDNA) deletions. Recently, CHCHD2 mutations are linked with autosomal dominant and sporadic Parkinson's disease (PD). The CHCHD2 is a multifunctional protein and plays roles in regulation of mitochondrial metabolism, synthesis of respiratory chain components, and modulation of cell apoptosis. With a better understanding of the pathophysiologic roles of CHCHD proteins, they may be potential novel therapeutic targets for human neurodegenerative diseases.

The cdk7-cyclin H-MAT1 complex associated with TFIIH is localized in coiled bodies.

PubMed Central

Jordan, P; Cunha, C; Carmo-Fonseca, M

1997-01-01

TFIIH is a general transcription factor for RNA polymerase II that in addition is involved in DNA excision repair. TFIIH is composed of eight or nine subunits and we show that at least four of them, namely cdk7, cyclin H, MAT1, and p62 are localized in the coiled body, a distinct subnuclear structure that is transcription dependent and highly enriched in small nuclear ribonucleoproteins. Although coiled bodies do not correspond to sites of transcription, in vivo incorporation of bromo-UTP shows that they are surrounded by transcription foci. Immunofluorescence analysis using antibodies directed against the essential repair factors proliferating cell nuclear antigen and XPG did not reveal labeling of the coiled body in either untreated cells or cells irradiated with UV light, arguing that coiled bodies are probably not involved in DNA repair mechanisms. The localization of cyclin H in the coiled body was predominantly detected during the G1 and S-phases of the cell cycle, whereas in G2 coiled bodies were very small or not detected. Finally, both cyclin H and cdk7 did not colocalize with P80 coilin after disruption of the coiled body, indicating that these proteins are specifically targeted to the small nuclear ribonucleoprotein-containing domain. Images PMID:9243502

An atomic model of the tropomyosin cable on F-actin.

PubMed

Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William

2014-08-05

Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hydrogen-bonded turns in proteins: The case for a recount

PubMed Central

Panasik, Nick; Fleming, Patrick J.; Rose, George D.

2005-01-01

β-Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β-turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β-turn. Here, we identify potential hydrogen-bonded β-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither α-helix nor β-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded β-turns. In particular, 33% of coil library residues were classified as β-turns prior to minimization. After minimization, 45% of such residues could be classified as β-turns, with another 8% in 310 helixes (which closely resemble type III β-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure. PMID:16251367

Hydrogen-bonded turns in proteins: the case for a recount.

PubMed

Panasik, Nick; Fleming, Patrick J; Rose, George D

2005-11-01

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

Power dissipation in HTS coated conductor coils under the simultaneous action of AC and DC currents and fields

NASA Astrophysics Data System (ADS)

Shen, Boyang; Li, Chao; Geng, Jianzhao; Zhang, Xiuchang; Gawith, James; Ma, Jun; Liu, Yingzhen; Grilli, Francesco; Coombs, T. A.

2018-07-01

This paper presents a comprehensive alternating current (AC) loss study of a circular high temperature superconductor (HTS) coated conductor coil. The AC losses from a circular double pancake coil were measured using the electrical method. A 2D axisymmetric H -formulation model using the FEM package in COMSOL Multiphysics has been established to match the circular geometry of the coil used in the experiment. Three scenarios have been analysed: Scenario 1 with AC transport current and DC magnetic field (experiment and simulation); Scenario 2 with DC transport current and AC magnetic field (simulation); and Scenario 3 with AC transport current and AC magnetic field (simulation and experimental data support). The angular dependence analysis on the coil under a magnetic field with different orientation angle θ has been carried out for all three scenarios. For Scenario 3, the effect of the relative phase difference Δφ between the AC current and the AC field on the total AC loss of the coil has been investigated. In summary, a current/field/angle/phase dependent AC loss ( I , B , θ, Δφ) study of a circular HTS coil has been carried out. The obtained results provide useful indications for the future design and research of HTS AC systems.

Cryogenic techniques for large superconducting magnets in space

NASA Technical Reports Server (NTRS)

Green, M. A.

1989-01-01

A large superconducting magnet is proposed for use in a particle astrophysics experiment, ASTROMAG, which is to be mounted on the United States Space Station. This experiment will have a two-coil superconducting magnet with coils which are 1.3 to 1.7 meters in diameter. The two-coil magnet will have zero net magnetic dipole moment. The field 15 meters from the magnet will approach earth's field in low earth orbit. The issue of high Tc superconductor will be discussed in the paper. The reasons for using conventional niobium-titanium superconductor cooled with superfluid helium will be presented. Since the purpose of the magnet is to do particle astrophysics, the superconducting coils must be located close to the charged particle detectors. The trade off between the particle physics possible and the cryogenic insulation around the coils is discussed. As a result, the ASTROMAG magnet coils will be operated outside of the superfluid helium storage tank. The fountain effect pumping system which will be used to cool the coil is described in the report. Two methods for extending the operating life of the superfluid helium dewar are discussed. These include: operation with a third shield cooled to 90 K with a sterling cycle cryocooler, and a hybrid cryogenic system where there are three hydrogen-cooled shields and cryostat support heat intercept points.

A novel no-insulation winding technique of high temperature-superconducting racetrack coil for rotating applications: A progress report in Korea university.

PubMed

Choi, Y H; Song, J B; Yang, D G; Kim, Y G; Hahn, S; Lee, H G

2016-10-01

This paper presents our recent progress on core technology development for a megawatt-class superconducting wind turbine generator supported by the international collaborative R&D program of the Korea Institute of Energy Technology Evaluation and Planning. To outperform the current high-temperature-superconducting (HTS) magnet technology in the wind turbine industry, a novel no-insulation winding technique was first proposed to develop the second-generation HTS racetrack coil for rotating applications. Here, we briefly report our recent studies on no-insulation (NI) winding technique for GdBCO coated conductor racetrack coils in the following areas: (1) Charging-discharging characteristics of no-insulation GdBCO racetrack coils with respect to external pressures applied to straight sections; (2) thermal and electrical stabilities of no-insulation GdBCO racetrack coils encapsulated with various impregnating materials; (3) quench behaviors of no-insulation racetrack coils wound with GdBCO conductor possessing various lamination layers; (4) electromagnetic characteristics of no-insulation GdBCO racetrack coils under time-varying field conditions. Test results confirmed that this novel NI winding technique was highly promising. It could provide development of a compact, mechanically dense, and self-protecting GdBCO magnet for use in real-world superconducting wind turbine generators.

Static Measurements on HTS Coils of Fully Superconducting AC Electric Machines for Aircraft Electric Propulsion System

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.; Hunker, Keith R.; Hartwig, Jason; Brown, Gerald V.

2017-01-01

The NASA Glenn Research Center (GRC) has been developing the high efficiency and high-power density superconducting (SC) electric machines in full support of electrified aircraft propulsion (EAP) systems for a future electric aircraft. A SC coil test rig has been designed and built to perform static and AC measurements on BSCCO, (RE)BCO, and YBCO high temperature superconducting (HTS) wire and coils at liquid nitrogen (LN2) temperature. In this paper, DC measurements on five SC coil configurations of various geometry in zero external magnetic field are measured to develop good measurement technique and to determine the critical current (Ic) and the sharpness (n value) of the super-to-normal transition. Also, standard procedures for coil design, fabrication, coil mounting, micro-volt measurement, cryogenic testing, current control, and data acquisition technique were established. Experimentally measured critical currents are compared with theoretical predicted values based on an electric-field criterion (Ec). Data here are essential to quantify the SC electric machine operation limits where the SC begins to exhibit non-zero resistance. All test data will be utilized to assess the feasibility of using HTS coils for the fully superconducting AC electric machine development for an aircraft electric propulsion system.

A novel no-insulation winding technique of high temperature-superconducting racetrack coil for rotating applications: A progress report in Korea university

NASA Astrophysics Data System (ADS)

Choi, Y. H.; Song, J. B.; Yang, D. G.; Kim, Y. G.; Hahn, S.; Lee, H. G.

2016-10-01

This paper presents our recent progress on core technology development for a megawatt-class superconducting wind turbine generator supported by the international collaborative R&D program of the Korea Institute of Energy Technology Evaluation and Planning. To outperform the current high-temperature-superconducting (HTS) magnet technology in the wind turbine industry, a novel no-insulation winding technique was first proposed to develop the second-generation HTS racetrack coil for rotating applications. Here, we briefly report our recent studies on no-insulation (NI) winding technique for GdBCO coated conductor racetrack coils in the following areas: (1) Charging-discharging characteristics of no-insulation GdBCO racetrack coils with respect to external pressures applied to straight sections; (2) thermal and electrical stabilities of no-insulation GdBCO racetrack coils encapsulated with various impregnating materials; (3) quench behaviors of no-insulation racetrack coils wound with GdBCO conductor possessing various lamination layers; (4) electromagnetic characteristics of no-insulation GdBCO racetrack coils under time-varying field conditions. Test results confirmed that this novel NI winding technique was highly promising. It could provide development of a compact, mechanically dense, and self-protecting GdBCO magnet for use in real-world superconducting wind turbine generators.

Insight into the Supramolecular Architecture of Intact Diatom Biosilica from DNP-Supported Solid-State NMR Spectroscopy.

PubMed

Jantschke, Anne; Koers, Eline; Mance, Deni; Weingarth, Markus; Brunner, Eike; Baldus, Marc

2015-12-07

Diatom biosilica is an inorganic/organic hybrid with interesting properties. The molecular architecture of the organic material at the atomic and nanometer scale has so far remained unknown, in particular for intact biosilica. A DNP-supported ssNMR approach assisted by microscopy, MS, and MD simulations was applied to study the structural organization of intact biosilica. For the first time, the secondary structure elements of tightly biosilica-associated native proteins in diatom biosilica were characterized in situ. Our data suggest that these proteins are rich in a limited set of amino acids and adopt a mixture of random-coil and β-strand conformations. Furthermore, biosilica-associated long-chain polyamines and carbohydrates were characterized, thereby leading to a model for the supramolecular organization of intact biosilica. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evidence for a role of SNX16 in regulating traffic between the early and later endosomal compartments.

PubMed

Hanson, Brendon J; Hong, Wanjin

2003-09-05

Sorting nexins (SNXs) are a growing family of proteins characterized by the presence of a PX domain. The PX domain mediates membrane association by interaction with phosphoinositides. The SNXs are generally believed to participate in membrane trafficking, but information regarding the function of individual proteins is limited. In this report, we describe the major characteristics of one member, SNX16. SNX16 is a novel 343-amino acid protein consisting of a central PX domain followed by a potential coiled-coil domain and a C-terminal region. Like other sorting nexins, SNX16 associates with the membrane via the PX domain which interacts with the phospholipid phosphatidylinositol 3-phosphate. We show via biochemical and cellular studies that SNX16 is distributed in both early and late endosome/lysosome structures. The coiled-coil domain is necessary for localization to the later endosomal structures, as mutant SNX16 lacking this domain was found only in early endosomes. Trafficking of internalized epidermal growth factor was also delayed by this SNX16 mutant, as these cells showed a delay in the segregation of epidermal growth factor in the early endosome for its delivery to later compartments. In addition, the coiled-coil domain is shown here to be important for homo-oligomerization of SNX16. Taken together, these results suggest that SNX16 is a sorting nexin that may function in the trafficking of proteins between the early and late endosomal compartments.

PspF-binding domain PspA1-144 and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.

PubMed

Osadnik, Hendrik; Schöpfel, Michael; Heidrich, Eyleen; Mehner, Denise; Lilie, Hauke; Parthier, Christoph; Risselada, H Jelger; Grubmüller, Helmut; Stubbs, Milton T; Brüser, Thomas

2015-11-01

Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer-binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ(54) -dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiologic tasks via coiled-coil domains. © 2015 John Wiley & Sons Ltd.

Improved Separations of Proteins and Sugar Derivatives Using the Small-Scale Cross-Axis Coil Planet Centrifuge with Locular Multilayer Coiled Columns

PubMed Central

Shinomiya, Kazufusa; Umezawa, Motoki; Seki, Manami; Nitta, Jun; Zaima, Kazumasa; Harikai, Naoki; Ito, Yoichiro

2016-01-01

1) Background Countercurrent chromatography (CCC) is liquid-liquid partition chromatography without using a solid support matrix. This technique requires further improvement of partition efficiency and shortening theseparation time. 2) Methods The locular multilayer coils modified with and without mixer glass beads were developed for the separation of proteins and 4-methylumbelliferyl (MU) sugar derivatives using the small-scale cross-axis coil planet centrifuge. 3) Results Proteins were well separated from each other and the separation was improved at a low flow rate of the mobile phase. On the other hand, 4-MU sugar derivatives were sufficiently resolved with short separation time at a highflow rate of the mobile phase under satisfactory stationary phase retention. 4) Conclusion Effective separations were achieved using the locular multilayer coil for proteins with aqueous-aqueous polymer phase systems and for 4-MU sugar derivatives with organic-aqueous two-phase solvent systems by inserting a glass bead into each locule. PMID:27891507

Electron cyclotron resonance ion sources with arc-shaped coils.

PubMed

Suominen, P; Wenander, F

2008-02-01

The minimum-B magnetic field structure of electron cyclotron resonance ion sources (ECRIS) has conventionally been formed with a combination of solenoids and a hexapole magnet. However, minimum-B structure can also be formed with arc-shaped coils. Recently it was shown that multiply charged heavy-ions can be produced with an ECRIS based on such a structure. In the future, the ARC-ECRIS magnetic field structure can be an interesting option for radioactive ion-beam sources and charge-breeders as well as for high performance ECRIS allowing for 100 GHz plasma heating. This paper presents some design aspects of the ARC-ECRIS.

The force control and path planning of electromagnetic induction-based massage robot.

PubMed

Wang, Wendong; Zhang, Lei; Li, Jinzhe; Yuan, Xiaoqing; Shi, Yikai; Jiang, Qinqin; He, Lijing

2017-07-20

Massage robot is considered as an effective physiological treatment to relieve fatigue, improve blood circulation, relax muscle tone, etc. The simple massage equipment quickly spread into market due to low cost, but they are not widely accepted due to restricted massage function. Complicated structure and high cost caused difficulties for developing multi-function massage equipment. This paper presents a novel massage robot which can achieve tapping, rolling, kneading and other massage operations, and proposes an improved reciprocating path planning algorithm to improve massage effect. The number of coil turns, the coil current and the distance between massage head and yoke were chosen to investigate the influence on massage force by finite element method. The control system model of the wheeled massage robot was established, including control subsystem of the motor, path algorithm control subsystem, parameter module of the massage robot and virtual reality interface module. The improved reciprocating path planning algorithm was proposed to improve regional coverage rate and massage effect. The influence caused by coil current, the number of coil turns and the distance between massage head and yoke were simulated in Maxwell. It indicated that coil current has more important influence compared to the other two factors. The path planning simulation of the massage robot was completed in Matlab, and the results show that the improved reciprocating path planning algorithm achieved higher coverage rate than the traditional algorithm. With the analysis of simulation results, it can be concluded that the number of coil turns and the distance between the moving iron core and the yoke could be determined prior to coil current, and the force can be controllable by optimizing structure parameters of massage head and adjusting coil current. Meanwhile, it demonstrates that the proposed algorithm could effectively improve path coverage rate during massage operations, therefore the massage effect can be improved.

GBNV encoded movement protein (NSm) remodels ER network via C-terminal coiled coil domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Pratibha; Savithri, H.S., E-mail: bchss@biochem.iisc.ernet.in

Plant viruses exploit the host machinery for targeting the viral genome–movement protein complex to plasmodesmata (PD). The mechanism by which the non-structural protein m (NSm) of Groundnut bud necrosis virus (GBNV) is targeted to PD was investigated using Agrobacterium mediated transient expression of NSm and its fusion proteins in Nicotiana benthamiana. GFP:NSm formed punctuate structures that colocalized with mCherry:plasmodesmata localized protein 1a (PDLP 1a) confirming that GBNV NSm localizes to PD. Unlike in other movement proteins, the C-terminal coiled coil domain of GBNV NSm was shown to be involved in the localization of NSm to PD, as deletion of thismore » domain resulted in the cytoplasmic localization of NSm. Treatment with Brefeldin A demonstrated the role of ER in targeting GFP NSm to PD. Furthermore, mCherry:NSm co-localized with ER–GFP (endoplasmic reticulum targeting peptide (HDEL peptide fused with GFP). Co-expression of NSm with ER–GFP showed that the ER-network was transformed into vesicles indicating that NSm interacts with ER and remodels it. Mutations in the conserved hydrophobic region of NSm (residues 130–138) did not abolish the formation of vesicles. Additionally, the conserved prolines at positions 140 and 142 were found to be essential for targeting the vesicles to the cell membrane. Further, systematic deletion of amino acid residues from N- and C-terminus demonstrated that N-terminal 203 amino acids are dispensable for the vesicle formation. On the other hand, the C-terminal coiled coil domain when expressed alone could also form vesicles. These results suggest that GBNV NSm remodels the ER network by forming vesicles via its interaction through the C-terminal coiled coil domain. Interestingly, NSm interacts with NP in vitro and coexpression of these two proteins in planta resulted in the relocalization of NP to PD and this relocalization was abolished when the N-terminal unfolded region of NSm was deleted. Thus, the NSm interacts with NP via its N-terminal unfolded region and the NSm–NP complex could in turn interact with the ER membrane via the C-terminal coiled coil domain of NSm to form vesicles that are targeted to PD and there by assist the cell to cell movement of the viral genome complex. - Highlights: • GBNV NSm localizes to plasmodesmata via the C-terminal coiled coil domain. • GBNV NSm interacts with endoplasmic reticulum network and remodels it to vesicles. • The C-terminal coiled domain alone is responsible for vesicle formation. • The N-terminal unfolded region of NSm is involved in the re-localization of NP to PD.« less

The Mitosis and Neurodevelopment Proteins NDE1 and NDEL1 Form Dimers, Tetramers, and Polymers with a Folded Back Structure in Solution*

PubMed Central

Soares, Dinesh C.; Bradshaw, Nicholas J.; Zou, Juan; Kennaway, Christopher K.; Hamilton, Russell S.; Chen, Zhuo A.; Wear, Martin A.; Blackburn, Elizabeth A.; Bramham, Janice; Böttcher, Bettina; Millar, J. Kirsty; Barlow, Paul N.; Walkinshaw, Malcolm D.; Rappsilber, Juri; Porteous, David J.

2012-01-01

Paralogs NDE1 (nuclear distribution element 1) and NDEL1 (NDE-like 1) are essential for mitosis and neurodevelopment. Both proteins are predicted to have similar structures, based upon high sequence similarity, and they co-complex in mammalian cells. X-ray diffraction studies and homology modeling suggest that their N-terminal regions (residues 8–167) adopt continuous, extended α-helical coiled-coil structures, but no experimentally derived information on the structure of their C-terminal regions or the architecture of the full-length proteins is available. In the case of NDE1, no biophysical data exists. Here we characterize the structural architecture of both full-length proteins utilizing negative stain electron microscopy along with our established paradigm of chemical cross-linking followed by tryptic digestion, mass spectrometry, and database searching, which we enhance using isotope labeling for mixed NDE1-NDEL1. We determined that full-length NDE1 forms needle-like dimers and tetramers in solution, similar to crystal structures of NDEL1, as well as chain-like end-to-end polymers. The C-terminal domain of each protein, required for interaction with key protein partners dynein and DISC1 (disrupted-in-schizophrenia 1), includes a predicted disordered region that allows a bent back structure. This facilitates interaction of the C-terminal region with the N-terminal coiled-coil domain and is in agreement with previous results showing N- and C-terminal regions of NDEL1 and NDE1 cooperating in dynein interaction. It sheds light on recently identified mutations in the NDE1 gene that cause truncation of the encoded protein. Additionally, analysis of mixed NDE1-NDEL1 complexes demonstrates that NDE1 and NDEL1 can interact directly. PMID:22843697

Linear Rogowski coil

NASA Astrophysics Data System (ADS)

Nassisi, V.; Delle Side, D.

2017-02-01

Nowadays, the employment and development of fast current pulses require sophisticated systems to perform measurements. Rogowski coils are used to diagnose cylindrical shaped beams; therefore, they are designed and built with a toroidal structure. Recently, to perform experiments of radiofrequency biophysical stresses, flat transmission lines have been developed. Therefore, in this work we developed a linear Rogowski coil to detect current pulses inside flat conductors. The system is first approached by means of transmission line theory. We found that, if the pulse width to be diagnosed is comparable with the propagation time of the signal in the detector, it is necessary to impose a uniform current as input pulse, or to use short coils. We further analysed the effect of the resistance of the coil and the influence of its magnetic properties. As a result, the device we developed is able to record pulses lasting for some hundreds of nanoseconds, depending on the inductance, load impedance, and resistance of the coil. Furthermore, its response is characterized by a sub-nanosecond rise time (˜100 ps). The attenuation coefficient depends mainly on the turn number of the coil, while the fidelity of the response depends both on the magnetic core characteristics and on the current distribution along the plane conductors.

Analysis and Optimization of Four-Coil Planar Magnetically Coupled Printed Spiral Resonators.

PubMed

Khan, Sadeque Reza; Choi, GoangSeog

2016-08-03

High-efficiency power transfer at a long distance can be efficiently established using resonance-based wireless techniques. In contrast to the conventional two-coil-based inductive links, this paper presents a magnetically coupled fully planar four-coil printed spiral resonator-based wireless power-transfer system that compensates the adverse effect of low coupling and improves efficiency by using high quality-factor coils. A conformal architecture is adopted to reduce the transmitter and receiver sizes. Both square architecture and circular architectures are analyzed and optimized to provide maximum efficiency at a certain operating distance. Furthermore, their performance is compared on the basis of the power-transfer efficiency and power delivered to the load. Square resonators can produce higher measured power-transfer efficiency (79.8%) than circular resonators (78.43%) when the distance between the transmitter and receiver coils is 10 mm of air medium at a resonant frequency of 13.56 MHz. On the other hand, circular coils can deliver higher power (443.5 mW) to the load than the square coils (396 mW) under the same medium properties. The performance of the proposed structures is investigated by simulation using a three-layer human-tissue medium and by experimentation.

''Football'' test coil: a simulated service test of internally-cooled, cabled superconductor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marston, P.G.; Iwasa, Y.; Thome, R.J.

Internally-cooled, cabled superconductor, (ICCS), appears from small-scale tests to be a viable alternative to pool-boiling cooled superconductors for large superconducting magnets. Potential advantages may include savings in helium inventory, smaller structure and ease of fabrication. Questions remain, however, about the structural performance of these systems. The ''football'' test coil has been designed to simulate the actual ''field-current-stress-thermal'' operating conditions of a 25 ka ICCS in a commercial scale MHD magnet. The test procedure will permit demonstration of the 20 year cyclic life of such a magnet in less than 20 days. This paper describes the design, construction and test ofmore » that coil which is wound of copper-stabilized niobium-titanium cable in steel conduit. 2 refs.« less

MRI surface-coil pair with strong inductive coupling.

PubMed

Mett, Richard R; Sidabras, Jason W; Hyde, James S

2016-12-01

A novel inductively coupled coil pair was used to obtain magnetic resonance phantom images. Rationale for using such a structure is described in R. R. Mett et al. [Rev. Sci. Instrum. 87, 084703 (2016)]. The original rationale was to increase the Q-value of a small diameter surface coil in order to achieve dominant loading by the sample. A significant improvement in the vector reception field (VRF) is also seen. The coil assembly consists of a 3-turn 10 mm tall meta-metallic self-resonant spiral (SRS) of inner diameter 10.4 mm and outer diameter 15.1 mm and a single-loop equalization coil of 25 mm diameter and 2 mm tall. The low-frequency parallel mode was used in which the rf currents on each coil produce magnetic fields that add constructively. The SRS coil assembly was fabricated and data were collected using a tissue-equivalent 30% polyacrylamide phantom. The large inductive coupling of the coils produces phase-coherency of the rf currents and magnetic fields. Finite-element simulations indicate that the VRF of the coil pair is about 4.4 times larger than for a single-loop coil of 15 mm diameter. The mutual coupling between coils influences the current ratio between the coils, which in turn influences the VRF and the signal-to-noise ratio (SNR). Data on a tissue-equivalent phantom at 9.4 T show a total SNR increase of 8.8 over the 15 mm loop averaged over a 25 mm depth and diameter. The experimental results are shown to be consistent with the magnetic resonance theory of the emf induced by spins in a coil, the theory of inductively coupled resonant circuits, and the superposition principle. The methods are general for magnetic resonance and other types of signal detection and can be used over a wide range of operating frequencies.

Integrated solar collector

DOEpatents

Tchernev, Dimiter I.

1985-01-01

A solar collector having a copper panel in a contiguous space relationship with a condenser-evaporator heat exchanger located under the panel, the panel having a honeycomb-like structure on its interior defining individual cells which are filled with zeolite loaded, in its adsorbed condition, with 18 to 20% by weight of water. The interior of the panel and heat exchanger are maintained at subatmospheric pressure of about 0.1 to 1 psia. The panel and heat exchanger are insulated on their lateral sides and bottoms and on the top of the heat exchange. The panel has a black coating on its top which is exposed to and absorbs solar energy. Surrounding the insulation (which supports the panel) is an extruded aluminum framework which supports a pair of spaced-apart glass panels above the solar panel. Water in conduits from a system for heating or cooling or both is connected to flow into an inlet and discharge from outlet of a finned coil received within the heat exchanger. The collector panel provides heat during the day through desorption and condensing of water vapor from the heated solar panel in the heat exchanger and cools at night by the re-adsorption of the water vapor from the heat exchanger which lowers the absolute pressure within the system and cools the heat exchange coils by evaporation.

Evaluation of machine learning tools for inspection of steam generator tube structures using pulsed eddy current

NASA Astrophysics Data System (ADS)

Buck, J. A.; Underhill, P. R.; Morelli, J.; Krause, T. W.

2017-02-01

Degradation of nuclear steam generator (SG) tubes and support structures can result in a loss of reactor efficiency. Regular in-service inspection, by conventional eddy current testing (ECT), permits detection of cracks, measurement of wall loss, and identification of other SG tube degradation modes. However, ECT is challenged by overlapping degradation modes such as might occur for SG tube fretting accompanied by tube off-set within a corroding ferromagnetic support structure. Pulsed eddy current (PEC) is an emerging technology examined here for inspection of Alloy-800 SG tubes and associated carbon steel drilled support structures. Support structure hole size was varied to simulate uniform corrosion, while SG tube was off-set relative to hole axis. PEC measurements were performed using a single driver with an 8 pick-up coil configuration in the presence of flat-bottom rectangular frets as an overlapping degradation mode. A modified principal component analysis (MPCA) was performed on the time-voltage data in order to reduce data dimensionality. The MPCA scores were then used to train a support vector machine (SVM) that simultaneously targeted four independent parameters associated with; support structure hole size, tube off-centering in two dimensions and fret depth. The support vector machine was trained, tested, and validated on experimental data. Results were compared with a previously developed artificial neural network (ANN) trained on the same data. Estimates of tube position showed comparable results between the two machine learning tools. However, the ANN produced better estimates of hole inner diameter and fret depth. The better results from ANN analysis was attributed to challenges associated with the SVM when non-constant variance is present in the data.

Atlas of optimal coil orientation and position for TMS: A computational study.

PubMed

Gomez-Tames, Jose; Hamasaka, Atsushi; Laakso, Ilkka; Hirata, Akimasa; Ugawa, Yoshikazu

2018-04-17

Transcranial magnetic stimulation (TMS) activates target brain structures in a non-invasive manner. The optimal orientation of the TMS coil for the motor cortex is well known and can be estimated using motor evoked potentials. However, there are no easily measurable responses for activation of other cortical areas and the optimal orientation for these areas is currently unknown. This study investigated the electric field strength, optimal coil orientation, and relative locations to optimally stimulate the target cortex based on computed electric field distributions. A total of 518,616 stimulation scenarios were studied using realistic head models (2401 coil locations × 12 coil angles × 18 head models). Inter-subject registration methods were used to generate an atlas of optimized TMS coil orientations on locations on the standard brain. We found that the maximum electric field strength is greater in primary somatosensory cortex and primary motor cortex than in other cortical areas. Additionally, a universal optimal coil orientation applicable to most subjects is more feasible at the primary somatosensory cortex and primary motor cortex. We confirmed that optimal coil angle follows the anatomical shape of the hand motor area to realize personalized optimization of TMS. Finally, on average, the optimal coil positions for TMS on the scalp deviated 5.5 mm from the scalp points with minimum cortex-scalp distance. This deviation was minimal at the premotor cortex and primary motor cortex. Personalized optimal coil orientation is preferable for obtaining the most effective stimulation. Copyright © 2018. Published by Elsevier Inc.

A superconducting homopolar motor and generator—new approaches

NASA Astrophysics Data System (ADS)

Fuger, Rene; Matsekh, Arkadiy; Kells, John; Sercombe, D. B. T.; Guina, Ante

2016-03-01

Homopolar machines were the first continuously running electromechanical converters ever demonstrated but engineering challenges and the rapid development of AC technology prevented wider commercialisation. Recent developments in superconducting, cryogenic and sliding contact technology together with new areas of application have led to a renewed interest in homopolar machines. Some of the advantages of these machines are ripple free constant torque, pure DC operation, high power-to-weight ratio and that rotating magnets or coils are not required. In this paper we present our unique approach to high power and high torque homopolar electromagnetic turbines using specially designed high field superconducting magnets and liquid metal current collectors. The unique arrangement of the superconducting coils delivers a high static drive field as well as effective shielding for the field critical sliding contacts. The novel use of additional shielding coils reduces weight and stray field of the system. Liquid metal current collectors deliver a low resistance, stable and low maintenance sliding contact by using a thin liquid metal layer that fills a circular channel formed by the moving edge of a rotor and surrounded by a conforming stationary channel of the stator. Both technologies are critical to constructing high performance machines. Homopolar machines are pure DC devices that utilise only DC electric and magnetic fields and have no AC losses in the coils or the supporting structure. Guina Energy Technologies has developed, built and tested different motor and generator concepts over the last few years and has combined its experience to develop a new generation of homopolar electromagnetic turbines. This paper summarises the development process, general design parameters and first test results of our high temperature superconducting test motor.

Transcranial magnetic stimulation: Improved coil design for deep brain investigation

NASA Astrophysics Data System (ADS)

Crowther, L. J.; Marketos, P.; Williams, P. I.; Melikhov, Y.; Jiles, D. C.; Starzewski, J. H.

2011-04-01

This paper reports on a design for a coil for transcranial magnetic stimulation. The design shows potential for improving the penetration depth of the magnetic field, allowing stimulation of subcortical structures within the brain. The magnetic and induced electric fields in the human head have been calculated with finite element electromagnetic modeling software and compared with empirical measurements. Results show that the coil design used gives improved penetration depth, but also indicates the likelihood of stimulation of additional tissue resulting from the spatial distribution of the magnetic field.

MQXFS1 Quadrupole Fabrication Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ambrosio, G.; Anerella, M.; Bossert, R.

This report presents the fabrication and QC data of MQXFS1, the first short model of the low-beta quadrupoles (MQXF) for the LHC High Luminosity Upgrade. It describes the conductor, the coils, and the structure that make the MQXFS1 magnet. Qualification tests and non-conformities are also presented and discussed. The fabrication of MQXFS1 was started before the finalization of conductor and coil design for MQXF magnets. Two strand design were used (RRP 108/127 and RRP 132/169). Cable and coil cross-sections were “first generation”.

Why fibrous proteins are romantic.

PubMed

Cohen, C

1998-01-01

Here I give a personal account of the great history of fibrous protein structure. I describe how Astbury first recognized the essential simplicity of fibrous proteins and their paradigmatic role in protein structure. The poor diffraction patterns yielded by these proteins were then deciphered by Pauling, Crick, Ramachandran and others (in part by model building) to reveal alpha-helical coiled coils, beta-sheets, and the collagen triple helical coiled coil-all characterized by different local sequence periodicities. Longer-range sequence periodicities (or "magic numbers") present in diverse fibrous proteins, such as collagen, tropomyosin, paramyosin, myosin, and were then shown to account for the characteristic axial repeats observed in filaments of these proteins. More recently, analysis of fibrous protein structure has been extended in many cases to atomic resolution, and some systems, such as "leucine zippers," are providing a deeper understanding of protein design than similar studies of globular proteins. In the last sections, I provide some dramatic examples of fibrous protein dynamics. One example is the so-called "spring-loaded" mechanism for viral fusion by the hemagglutinin protein of influenza. Another is the possible conformational changes in prion proteins, implicated in "mad cow disease," which may be related to similar transitions in a variety of globular and fibrous proteins. Copyright 1998 Academic Press.

Analytical model of tilted driver–pickup coils for eddy current nondestructive evaluation

NASA Astrophysics Data System (ADS)

Cao, Bing-Hua; Li, Chao; Fan, Meng-Bao; Ye, Bo; Tian, Gui-Yun

2018-03-01

A driver-pickup probe possesses better sensitivity and flexibility due to individual optimization of a coil. It is frequently observed in an eddy current (EC) array probe. In this work, a tilted non-coaxial driver-pickup probe above a multilayered conducting plate is analytically modeled with spatial transformation for eddy current nondestructive evaluation. Basically, the core of the formulation is to obtain the projection of magnetic vector potential (MVP) from the driver coil onto the vector along the tilted pickup coil, which is divided into two key steps. The first step is to make a projection of MVP along the pickup coil onto a horizontal plane, and the second one is to build the relationship between the projected MVP and the MVP along the driver coil. Afterwards, an analytical model for the case of a layered plate is established with the reflection and transmission theory of electromagnetic fields. The calculated values from the resulting model indicate good agreement with those from the finite element model (FEM) and experiments, which validates the developed analytical model. Project supported by the National Natural Science Foundation of China (Grant Nos. 61701500, 51677187, and 51465024).

Open-Access, Low-Magnetic-Field MRI System for Lung Research

NASA Technical Reports Server (NTRS)

Mair, Ross W.; Rosen, Matthew S.; Tsai, Leo L.; Walsworth, Ronald L.; Hrovat, Mirko I.; Patz, Samuel; Ruset, Iullian C.; Hersman, F. William

2009-01-01

An open-access magnetic resonance imaging (MRI) system is being developed for use in research on orientational/gravitational effects on lung physiology and function. The open-access geometry enables study of human subjects in diverse orientations. This system operates at a magnetic flux density, considerably smaller than the flux densities of typical other MRI systems, that can be generated by resistive electromagnet coils (instead of the more-expensive superconducting coils of the other systems). The human subject inhales air containing He-3 or Xe-129 atoms, the nuclear spins of which have been polarized by use of a laser beam to obtain a magnetic resonance that enables high-resolution gas space imaging at the low applied magnetic field. The system includes a bi-planar, constant-current, four-coil electromagnet assembly and associated electronic circuitry to apply a static magnetic field of 6.5 mT throughout the lung volume; planar coils and associated circuitry to apply a pulsed magnetic-field-gradient for each spatial dimension; a single, detachable radio-frequency coil and associated circuitry for inducing and detecting MRI signals; a table for supporting a horizontal subject; and electromagnetic shielding surrounding the electromagnet coils.

Rho-associated coiled-coil containing kinases (ROCK)

PubMed Central

Julian, Linda; Olson, Michael F

2014-01-01

Rho-associated coiled-coil containing kinases (ROCK) were originally identified as effectors of the RhoA small GTPase.1–5 They belong to the AGC family of serine/threonine kinases6 and play vital roles in facilitating actomyosin cytoskeleton contractility downstream of RhoA and RhoC activation. Since their discovery, ROCK kinases have been extensively studied, unveiling their manifold functions in processes including cell contraction, migration, apoptosis, survival, and proliferation. Two mammalian ROCK homologs have been identified, ROCK1 (also called ROCK I, ROKβ, Rho-kinase β, or p160ROCK) and ROCK2 (also known as ROCK II, ROKα, or Rho kinase), hereafter collectively referred to as ROCK. In this review, we will focus on the structure, regulation, and functions of ROCK. PMID:25010901

Numerical simulations on active shielding methods comparison and wrapped angle optimization for gradient coil design in MRI with enhanced shielding effect

NASA Astrophysics Data System (ADS)

Wang, Yaohui; Xin, Xuegang; Guo, Lei; Chen, Zhifeng; Liu, Feng

2018-05-01

The switching of a gradient coil current in magnetic resonance imaging will induce an eddy current in the surrounding conducting structures while the secondary magnetic field produced by the eddy current is harmful for the imaging. To minimize the eddy current effects, the stray field shielding in the gradient coil design is usually realized by minimizing the magnetic fields on the cryostat surface or the secondary magnetic fields over the imaging region. In this work, we explicitly compared these two active shielding design methods. Both the stray field and eddy current on the cryostat inner surface were quantitatively discussed by setting the stray field constraint with an ultra-low maximum intensity of 2 G and setting the secondary field constraint with an extreme small shielding ratio of 0.000 001. The investigation revealed that the secondary magnetic field control strategy can produce coils with a better performance. However, the former (minimizing the magnetic fields) is preferable when designing a gradient coil with an ultra-low eddy current that can also strictly control the stray field leakage at the edge of the cryostat inner surface. A wrapped-edge gradient coil design scheme was then optimized for a more effective control of the stray fields. The numerical simulation on the wrapped-edge coil design shows that the optimized wrapping angles for the x and z coils in terms of our coil dimensions are 40° and 90°, respectively.

Midbody Targeting of the ESCRT Machinery by a Noncanonical Coiled Coil in CEP55

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hyung Ho; Elia, Natalie; Ghirlando, Rodolfo

2008-11-14

The ESCRT (endosomal sorting complex required for transport) machinery is required for the scission of membrane necks in processes including the budding of HIV-1 and cytokinesis. An essential step in cytokinesis is recruitment of the ESCRT-I complex and the ESCRT-associated protein ALIX to the midbody (the structure that tethers two daughter cells) by the protein CEP55. Biochemical experiments show that peptides from ALIX and the ESCRT-I subunit TSG101 compete for binding to the ESCRT and ALIX-binding region (EABR) of CEP55. We solved the crystal structure of EABR bound to an ALIX peptide at a resolution of 2.0 angstroms. The structuremore » shows that EABR forms an aberrant dimeric parallel coiled coil. Bulky and charged residues at the interface of the two central heptad repeats create asymmetry and a single binding site for an ALIX or TSG101 peptide. Both ALIX and ESCRT-I are required for cytokinesis, which suggests that multiple CEP55 dimers are required for function.« less

Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Zhiqiang; Su, Lijing; Pei, Jimin

In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices,more » are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.« less

The homo-oligomerisation of both Sas-6 and Ana2 is required for efficient centriole assembly in flies

PubMed Central

Cottee, Matthew A; Muschalik, Nadine; Johnson, Steven; Leveson, Joanna; Raff, Jordan W; Lea, Susan M

2015-01-01

Sas-6 and Ana2/STIL proteins are required for centriole duplication and the homo-oligomerisation properties of Sas-6 help establish the ninefold symmetry of the central cartwheel that initiates centriole assembly. Ana2/STIL proteins are poorly conserved, but they all contain a predicted Central Coiled-Coil Domain (CCCD). Here we show that the Drosophila Ana2 CCCD forms a tetramer, and we solve its structure to 0.8 Å, revealing that it adopts an unusual parallel-coil topology. We also solve the structure of the Drosophila Sas-6 N-terminal domain to 2.9 Å revealing that it forms higher-order oligomers through canonical interactions. Point mutations that perturb Sas-6 or Ana2 homo-oligomerisation in vitro strongly perturb centriole assembly in vivo. Thus, efficient centriole duplication in flies requires the homo-oligomerisation of both Sas-6 and Ana2, and the Ana2 CCCD tetramer structure provides important information on how these proteins might cooperate to form a cartwheel structure. DOI: http://dx.doi.org/10.7554/eLife.07236.001 PMID:26002084

Ex vivo mouse brain microscopy at 15T with loop-gap RF coil.

PubMed

Cohen, Ouri; Ackerman, Jerome L

2018-04-18

The design of a loop-gap-resonator RF coil optimized for ex vivo mouse brain microscopy at ultra high fields is described and its properties characterized using simulations, phantoms and experimental scans of mouse brains fixed in 10% formalin containing 4 mM Magnevist™. The RF (B 1 ) and magnetic field (B 0 ) homogeneities are experimentally quantified and compared to electromagnetic simulations of the coil. The coil's performance is also compared to a similarly sized surface coil and found to yield double the sensitivity. A three-dimensional gradient-echo (GRE) sequence is used to acquire high resolution mouse brain scans at (47 μm) 3 resolution in 1.8 h and a 20 × 20 × 19 μm 3 resolution in 27 h. The high resolution obtained permitted clear visualization and identification of multiple structures in the ex vivo mouse brain and represents, to our knowledge, the highest resolution ever achieved for a whole mouse brain. Importantly, the coil design is simple and easy to construct. Copyright © 2018 Elsevier Inc. All rights reserved.

SAR and thermal response effects of a two-arm Archimedean spiral coil in a magnetic induction sensor on a human head.

PubMed

Zhang, Ziyi; Liu, Peiguo; Zhou, Dongming; Zhang, Liang; Ding, Liang

2015-01-01

This study investigates the radiation safety of a newly designed magnetic induction sensor. This novel magnetic induction sensor uses a two-arm Archimedean spiral coil (TAASC) as the exciter. A human head model with a real anatomical structure was used to calculate the specific absorption rate (SAR) and temperature change. Computer Simulation Technology (CST) was used to determine the values of the peak 10-g SAR under different operating parameters (current, frequency, horizontal distance between the excitation coil and the receiver coil, vertical distance between the top of the head model and the XOY plane, position of excitation coil, and volume of hemorrhage). Then, the highest response for the SAR and temperature rise was determined. The results showed that this new magnetic induction sensor is safe in the initial state; for safety reasons, the TAASC current should not exceed 4 A. The scalp tissue absorbed most of the electromagnetic energy. The TAASC's SAR/thermal performance was close to that of the circular coil.

Self-assembled nanocages based on the coiled coil bundle motif

NASA Astrophysics Data System (ADS)

Sinha, Nairiti; Villegas, Jose; Saven, Jeffery; Kiick, Kristi; Pochan, Darrin

Computational design of coiled coil peptide bundles that undergo solution phase self-assembly presents a diverse toolbox for engineering new materials with tunable and pre-determined nanostructures that can have various end applications such as in drug delivery, biomineralization and electronics. Self-assembled cages are especially advantageous as the cage geometry provides three distinct functional sites: the interior, the exterior and the solvent-cage interface. In this poster, syntheses and characterization of a peptide cage based on computationally designed homotetrameric coiled coil bundles as building blocks is discussed. Techniques such as Transmission Electron Microscopy (TEM), Small-Angle Neutron Scattering (SANS) and Analytical Ultracentrifugation (AUC) are employed to characterize the size, shape and molecular weight of the self-assembled peptide cages under different pH and temperature conditions. Various self-assembly pathways such as dialysis and thermal quenching are shown to have a significant impact on the final structure of these peptides in solution. Comparison of results with the target cage design can be used to iteratively improve the peptide design and provide greater understanding of its interactions and folding.

Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine.

PubMed

Tang, Y; Ghirlanda, G; Vaidehi, N; Kua, J; Mainz, D T; Goddard III, W A; DeGrado, W F; Tirrell, D A

2001-03-06

Substitution of leucine residues by 5,5,5-trifluoroleucine at the d-positions of the leucine zipper peptide GCN4-p1d increases the thermal stability of the coiled-coil structure. The midpoint thermal unfolding temperature of the fluorinated peptide is elevated by 13 degrees C at 30 microM peptide concentration. The modified peptide is more resistant to chaotropic denaturants, and the free energy of folding of the fluorinated peptide is 0.5-1.2 kcal/mol larger than that of the hydrogenated form. A similarly fluorinated form of the DNA-binding peptide GCN4-bZip binds to target DNA sequences with affinity and specificity identical to those of the hydrogenated form, while demonstrating enhanced thermal stability. Molecular dynamics simulation on the fluorinated GCN4-p1d peptide using the Surface Generalized Born implicit solvation model revealed that the coiled-coil binding energy is 55% more favorable upon fluorination. These results suggest that fluorination of hydrophobic substructures in peptides and proteins may provide new means of increasing protein stability, enhancing protein assembly, and strengthening receptor-ligand interactions.

A super-cusp divertor configuration for tokamaks

DOE PAGES

Ryutov, D. D.

2015-08-26

Our study demonstrates a remarkable flexibility of advanced divertor configurations created with the remote poloidal field coils. The emphasis here is on the configurations with three poloidal field nulls in the divertor area. We are seeking the structures where all three nulls lie on the same separatrix, thereby creating two zones of a very strong flux expansion, as envisaged in the concept of Takase’s cusp divertor. It turns out that the set of remote coils can produce a cusp divertor, with additional advantages of: (i) a large stand-off distance between the divertor and the coils and (ii) a thorough controlmore » that these coils exert over the fine features of the configuration. In reference to these additional favourable properties acquired by the cusp divertor, the resulting configuration could be called ‘a super-cusp’. General geometrical features of the three-null configurations produced by remote coils are described. Furthermore, issues on the way to practical applications include the need for a more sophisticated control system and possible constraints related to excessively high currents in the divertor coils.« less

Clamp for use in winding large magnet coils

DOEpatents

Brown, Robert L.; Kenney, Walter J.

1983-01-01

In one aspect, the invention is a novel arrangement for applying forces to urns of a vertically extending helical coil which is wound about a support. The apparatus includes a first rigid member extending towards the turns. A second rigid member extends transversely from the end of the first and has a vertically extending face provided with a generally straight groove extending transversely of the turns. A longitudinal passage in the first member connects to the groove to form therewith a continuous guideway for rollable articles. A rigid lug longitudinally movable in the groove is provided with a projection which extends out of the groove and beneath the bottom of a selected turn of the coil. A train of rigid, rollable articles is disposed in the guideway inwardly of the lug. Means are provided for applying force to that end of the train which is relatively remote from the lug, to urge the latter against the bottom face of the selected turn. As a result, that turn is moved upward along the face of the support, establishing a selected spacing between that turn and the previously formed turn of the coil. When upward movement of the selected turn stops, the force applied to the lug immediately translates to a force which urges the above-mentioned grooved face against all of the formed turns, thus compressing them against the support. The above-mentioned first and second members are swingably mounted so that they can be temporarily moved out of the winding path, thus permitting continuous winding.

Clamp for use in winding large magnet coils

DOEpatents

Brown, R.L.; Kenney, W.J.

1981-05-05

In one aspect, the invention is a novel arrangement for applying forces to turns of a vertically extending helical coil which is wound about a support. The apparatus includes a first rigid member extending towards the turns. A second rigid member extends transversely from the end of the first and has a vertically extending face provided with a generally straight groove extending transversely of the turns. A longitudinal passage in the first member connects to the groove to form therewith a continuous guideway for rollable articles. A rigid lug longitudinally movable in the groove is provided with a projection which extends out of the groove and beneath the bottom of a selected turn of the coil. A train of rigid, rollable articles is disposed in the guideway inwardly of the lug. Means are provided for applying force to that end of the train which is relatively remote from the lug, to urge the latter against the bottom face of the selected turn. As a result, that turn is moved upward along the face of the support, establishing a selected spacing between that turn and the previously formed turn of the coil. When upward movement of the selected turn stops, the force applied to the lug immediately translates to a force which urges the above-mentioned grooved face against all of the formed turns, thus compressing them against the support. The above-mentioned first and second members are swingably mounted so that they can be temporarily moved out of the winding path, thus permitting continuous winding.

Structure and Dynamics of Helical Protein Fragments Investigated by Theory and Experiment

NASA Astrophysics Data System (ADS)

Karimi, Afshin

This work addresses the conformation and dynamics of model peptides using spectroscopy and molecular dynamics simulations. Experimentally, we investigate the structure and dynamics of peptide fragments taken from coiled coil and three helical bundle motifs of bacterial coat proteins. Theoretically, we use molecular dynamics simulations of isolated helices with explicit water molecules to derive trajectories which reveal features about picosecond dynamics and local unfolding events. The assignment of the ^1H, ^{15}N, and ^ {13}C resonances, secondary structure, backbone dynamics, hydration and other biophysical parameters of a 30 residue recombinant peptide corresponding to an immunogenic site on the coiled coil region of Streptococcus pyogenes 24M protein are reported. Our results suggest that this peptide is a symmetric parallel dimeric alpha-helical coiled coil with local defects within the helix and fraying at the termini. The ^1H and ^ {15}N assignments, the hydration, the overall fold, and other biophysical parameters of a recombinant B domain of Staphylococcal protein A (FB) are reported. Our results indicate FB is a highly stable monomeric three helical bundle. A symmetric two domain construct was used to probe the modular assembly of two B domains. Here, spectroscopic results suggest weak interactions between the two domains. The folding pathway of FB was investigated using amide exchange data of the native protein and peptide models. We propose that the helical hairpin consisting of helices II and III is an on-pathway intermediate in the folding of FB. Two 1 ns molecular dynamics simulations (MD) on two mainly helical peptides--an 18 residue peptide corresponding to a portion of the H helix of myoglobin (MBH) and a 14 residue analogue of the C-peptide of ribonuclease A (CRNA) --were carried out in water using the united atom AMBER/OPLS force-field. In the case of MBH, the initial helical conformation progressively frays to a more disordered structure. A common motif in the unfolding mechanism involves the formation of transient turn structures involving several water molecules. In contrast to the MBH simulation, the CRNA trajectory was characterized by the presence of fairly stable i ... i+4 (alpha-helical) hydrogen bonds throughout the simulation, except at the N-terminus where some fraying was observed.

Molecular studies on structural changes and oligomerisation of violaxanthin de-epoxidase associated with the pH-dependent activation.

PubMed

Hallin, Erik Ingmar; Hasan, Mahmudul; Guo, Kuo; Åkerlund, Hans-Erik

2016-07-01

Violaxanthin de-epoxidase (VDE) is a conditionally soluble enzyme located in the thylakoid lumen and catalyses the conversion of violaxanthin to antheraxanthin and zeaxanthin, which are located in the thylakoid membrane. These reactions occur when the plant or algae are exposed to saturating light and the zeaxanthin formed is involved in the process of non-photochemical quenching that protects the photosynthetic machinery during stress. Oversaturation by light results in a reduction of the pH inside the thylakoids, which in turn activates VDE and the de-epoxidation of violaxanthin. To elucidate the structural events responsible for the pH-dependent activation of VDE, full length and truncated forms of VDE were studied at different pH using circular dichroism (CD) spectroscopy, crosslinking and small angle X-ray scattering (SAXS). CD spectroscopy showed the formation of α-helical coiled-coil structure, localised in the C-terminal domain. Chemical crosslinking of VDE showed that oligomers were formed at low pH, and suggested that the position of the N-terminal domain is located near the opening of lipocalin-like barrel, where violaxanthin has been predicted to bind. SAXS was used to generate models of monomeric VDE at high pH and also a presumably dimeric structure of VDE at low pH. For the dimer, the best fit suggests that the interaction is dominated by one of the domains, preferably the C-terminal domain due to the lost ability to oligomerise at low pH, shown in earlier studies, and the predicted formation of coiled-coil structure.

Test results of a Nb 3Al/Nb 3Sn subscale magnet for accelerator application

DOE PAGES

Iio, Masami; Xu, Qingjin; Nakamoto, Tatsushi; ...

2015-01-28

The High Energy Accelerator Research Organization (KEK) has been developing a Nb 3Al and Nb 3Sn subscale magnet to establish the technology for a high-field accelerator magnet. The development goals are a feasibility demonstration for a Nb 3Al cable and the technology acquisition of magnet fabrication with Nb 3Al superconductors. KEK developed two double-pancake racetrack coils with Rutherford-type cables composed of 28 Nb 3Al wires processed by rapid heating, quenching, and transformation in collaboration with the National Institute for Materials Science and the Fermi National Accelerator Laboratory. The magnet was fabricated to efficiently generate a high magnetic field in amore » minimum-gap common-coil configuration with two Nb 3Al coils sandwiched between two Nb 3Sn coils produced by the Lawrence Berkeley National Laboratory. A shell-based structure and a “bladder and key” technique have been used for adjusting coil prestress during both the magnet assembly and the cool down. In the first excitation test of the magnet at 4.5 K performed in June 2014, the highest quench current of the Nb 3Sn coil, i.e., 9667 A, was reached at 40 A/s corresponding to 9.0 T in the Nb 3Sn coil and 8.2 T in the Nb 3Al coil. The quench characteristics of the magnet were studied.« less

Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

PubMed

Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

2012-09-26

Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

De novo design of peptide immunogens that mimic the coiled coil region of human T-cell leukemia virus type-1 glycoprotein 21 transmembrane subunit for induction of native protein reactive neutralizing antibodies.

PubMed

Sundaram, Roshni; Lynch, Marcus P; Rawale, Sharad V; Sun, Yiping; Kazanji, Mirdad; Kaumaya, Pravin T P

2004-06-04

Peptide vaccines able to induce high affinity and protective neutralizing antibodies must rely in part on the design of antigenic epitopes that mimic the three-dimensional structure of the corresponding region in the native protein. We describe the design, structural characterization, immunogenicity, and neutralizing potential of antibodies elicited by conformational peptides derived from the human T-cell leukemia virus type 1 (HTLV-1) gp21 envelope glycoprotein spanning residues 347-374. We used a novel template design and a unique synthetic approach to construct two peptides (WCCR2T and CCR2T) that would each assemble into a triple helical coiled coil conformation mimicking the gp21 crystal structure. The peptide B-cell epitopes were grafted onto the epsilon side chains of three lysyl residues on a template backbone construct consisting of the sequence acetyl-XGKGKGKGCONH2 (where X represents the tetanus toxoid promiscuous T cell epitope (TT) sequence 580-599). Leucine substitutions were introduced at the a and d positions of the CCR2T sequence to maximize helical character and stability as shown by circular dichroism and guanidinium hydrochloride studies. Serum from an HTLV-1-infected patient was able to recognize the selected epitopes by enzyme-linked immunosorbent assay (ELISA). Mice immunized with the wild-type sequence (WCCR2T) and the mutant sequence (CCR2T) elicited high antibody titers that were capable of recognizing the native protein as shown by flow cytometry and whole virus ELISA. Sera and purified antibodies from immunized mice were able to reduce the formation of syncytia induced by the envelope glycoprotein of HTLV-1, suggesting that antibodies directed against the coiled coil region of gp21 are capable of disrupting cell-cell fusion. Our results indicate that these peptides represent potential candidates for use in a peptide vaccine against HTLV-1.

Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junin arenavirus envelope glycoprotein

DOE Office of Scientific and Technical Information (OSTI.GOV)

York, Joanne; Agnihothram, Sudhakar S.; Romanowski, Victor

2005-12-20

The G2 fusion subunit of the Junin virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins,more » four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell-cell fusion. Taken together, our results indicate that {alpha}-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever.« less

A magnetic resonance (MR) microscopy system using a microfluidically cryo-cooled planar coil.

PubMed

Koo, Chiwan; Godley, Richard F; Park, Jaewon; McDougall, Mary P; Wright, Steven M; Han, Arum

2011-07-07

We present the development of a microfluidically cryo-cooled planar coil for magnetic resonance (MR) microscopy. Cryogenically cooling radiofrequency (RF) coils for magnetic resonance imaging (MRI) can improve the signal to noise ratio (SNR) of the experiment. Conventional cryostats typically use a vacuum gap to keep samples to be imaged, especially biological samples, at or near room temperature during cryo-cooling. This limits how close a cryo-cooled coil can be placed to the sample. At the same time, a small coil-to-sample distance significantly improves the MR imaging capability due to the limited imaging depth of planar MR microcoils. These two conflicting requirements pose challenges to the use of cryo-cooling in MR microcoils. The use of a microfluidic based cryostat for localized cryo-cooling of MR microcoils is a step towards eliminating these constraints. The system presented here consists of planar receive-only coils with integrated cryo-cooling microfluidic channels underneath, and an imaging surface on top of the planar coils separated by a thin nitrogen gas gap. Polymer microfluidic channel structures fabricated through soft lithography processes were used to flow liquid nitrogen under the coils in order to cryo-cool the planar coils to liquid nitrogen temperature (-196 °C). Two unique features of the cryo-cooling system minimize the distance between the coil and the sample: (1) the small dimension of the polymer microfluidic channel enables localized cooling of the planar coils, while minimizing thermal effects on the nearby imaging surface. (2) The imaging surface is separated from the cryo-cooled planar coil by a thin gap through which nitrogen gas flows to thermally insulate the imaging surface, keeping it above 0 °C and preventing potential damage to biological samples. The localized cooling effect was validated by simulations, bench testing, and MR imaging experiments. Using this cryo-cooled planar coil system inside a 4.7 Tesla MR system resulted in an average image SNR enhancement of 1.47 ± 0.11 times relative to similar room-temperature coils. This journal is © The Royal Society of Chemistry 2011

A Magnetic Resonance (MR) Microscopy System using a Microfluidically Cryo-Cooled Planar Coil

PubMed Central

Koo, Chiwan; Godley, Richard F.; Park, Jaewon; McDougall, Mary P.; Wright, Steven M.; Han, Arum

2011-01-01

We present the development of a microfluidically cryo-cooled planar coil for magnetic resonance (MR) microscopy. Cryogenically cooling radiofrequency (RF) coils for magnetic resonance imaging (MRI) can improve the signal to noise ratio (SNR) of the experiment. Conventional cryostats typically use a vacuum gap to keep samples to be imaged, especially biological samples, at or near room temperature during cryo-cooling. This limits how close a cryo-cooled coil can be placed to the sample. At the same time, a small coil-to-sample distance significantly improves the MR imaging capability due to the limited imaging depth of planar MR microcoils. These two conflicting requirements pose challenges to the use of cryo-cooling in MR microcoils. The use of a microfluidic based cryostat for localized cryo-cooling of MR microcoils is a step towards eliminating these constraints. The system presented here consists of planar receive-only coils with integrated cryo-cooling microfluidic channels underneath, and an imaging surface on top of the planar coils separated by a thin nitrogen gas gap. Polymer microfluidic channel structures fabricated through soft lithography processes were used to flow liquid nitrogen under the coils in order to cryo-cool the planar coils to liquid nitrogen temperature (−196°C). Two unique features of the cryo-cooling system minimize the distance between the coil and the sample: 1) The small dimension of the polymer microfluidic channel enables localized cooling of the planar coils, while minimizing thermal effects on the nearby imaging surface. 2) The imaging surface is separated from the cryo-cooled planar coil by a thin gap through which nitrogen gas flows to thermally insulate the imaging surface, keeping it above 0°C and preventing potential damage to biological samples. The localized cooling effect was validated by simulations, bench testing, and MR imaging experiments. Using this cryo-cooled planar coil system inside a 4.7 Tesla MR system resulted in an average image SNR enhancement of 1.47 ± 0.11 times relative to similar room-temperature coils. PMID:21603723

Characterization of leucine zipper complexes by electrospray ionization mass spectrometry.

PubMed Central

Wendt, H.; Dürr, E.; Thomas, R. M.; Przybylski, M.; Bosshard, H. R.

1995-01-01

The development of "soft" ionization methods has enabled the mass spectrometric analysis of higher-order structural features of proteins. We have applied electrospray ionization mass spectrometry (ESI-MS) to the analysis of the number and composition of polypeptide chains in homomeric and heteromeric leucine zippers. In comparison with other methods that have been used to analyze leucine zippers, such as analytical ultracentrifugation, gel chromatography, or electrophoretic band shift assays, ESI-MS is very fast and highly sensitive and provides a straightforward way to distinguish between homomeric and heteromeric coiled-coil structures. ESI-MS analyses were carried out on the parallel dimeric leucine zipper domain GCN4-p1 of the yeast transcription factor GCN4 and on three synthetic peptides with the sequences Ac-EYEALEKKLAAX1EAKX2QALEKKLEALEHG-amide: peptide LZ (X1, X2 = Leu), peptide LZ(12A) (X1 = Ala, X2 = Leu), and peptide LZ(16N) (X1 = Leu, X2 = Asn). Equilibrium ultracentrifugation analysis showed that LZ forms a trimeric coiled coil and this could be confirmed unequivocally by ESI-MS as could the dimeric nature of GCN4-p1. The formation of heteromeric two- and three-stranded leucine zippers composed of chains from LZ and LZ(12A), or from GCN4-p1 and LZ, was demonstrated by ESI-MS and confirmed by fluorescence quenching experiments on fluorescein-labeled peptides. The results illustrate the adaptability and flexibility of the leucine zipper motif, properties that could be useful to the design of specific protein assemblies by way of coiled-coil domains. PMID:8520482

Analysis of field errors for LARP Nb 3Sn HQ03 quadrupole magnet

DOE PAGES

Wang, Xiaorong; Ambrosio, Giorgio; Chlachidze, Guram; ...

2016-12-01

The U.S. LHC Accelerator Research Program, in close collaboration with CERN, has developed three generations of high-gradient quadrupole (HQ) Nb 3Sn model magnets, to support the development of the 150 mm aperture Nb 3Sn quadrupole magnets for the High-Luminosity LHC. The latest generation, HQ03, featured coils with better uniformity of coil dimensions and properties than the earlier generations. We tested the HQ03 magnet at FNAL, including the field quality study. The profiles of low-order harmonics along the magnet aperture observed at 15 kA, 1.9 K can be traced back to the assembled coil pack before the magnet assembly. Based onmore » the measured harmonics in the magnet center region, the coil block positioning tolerance was analyzed and compared with earlier HQ01 and HQ02 magnets to correlate with coil and magnet fabrication. Our study the capability of correcting the low-order non-allowed field errors, magnetic shims were installed in HQ03. Furthermore, the expected shim contribution agreed well with the calculation. For the persistent-current effect, the measured a4 can be related to 4% higher in the strand magnetization of one coil with respect to the other three coils. Lastly, we compare the field errors due to the inter-strand coupling currents between HQ03 and HQ02.« less

A novel structural tree for wrap-proteins, a subclass of (α+β)-proteins.

PubMed

Boshkova, Eugenia A; Gordeev, Alexey B; Efimov, Alexander V

2014-01-01

In this paper, a novel structural subclass of (α+β)-proteins is presented. A characteristic feature of these proteins and domains is that they consist of strongly twisted and coiled β-sheets wrapped around one or two α-helices, so they are referred to here as wrap-proteins. It is shown that overall folds of the wrap-proteins can be obtained by stepwise addition of α-helices and/or β-strands to the strongly twisted and coiled β-hairpin taken as the starting structure in modeling. As a result of modeling, a structural tree for the wrap-proteins was constructed that includes 201 folds of which 49 occur in known nonhomologous proteins.

Magnetic suspension and balance system study

NASA Technical Reports Server (NTRS)

Boom, R. W.; Eyssa, Y. M.; Mcintosh, G. E.; Abdelsalam, M. K.

1984-01-01

A compact design for a superconducting magnetic suspension and balance system is developed for a 8 ft. x 8 ft. transonic wind tunnel. The main features of the design are: a compact superconducting solenoid in the suspended airplane model; permanent magnet wings; one common liquid helium dewar for all superconducting coils; efficient new race track coils for roll torques; use of established 11 kA cryostable AC conductor; acceptable AC losses during 10 Hz control even with all steel structure; and a 560 liter/hour helium liquefier. Considerable design simplicity, reduced magnet weights, and reduced heat leak results from using one common dewar which eliminates most heavy steel structure between coils and the suspended model. Operational availability is thought to approach 100% for such magnet systems. The weight and cost of the magnet system is approximately one-third that of previous less compact designs.

Multi-scale analysis and characterization of the ITER pre-compression rings

NASA Astrophysics Data System (ADS)

Foussat, A.; Park, B.; Rajainmaki, H.

2014-01-01

The toroidal field (TF) system of ITER Tokamak composed of 18 "D" shaped Toroidal Field (TF) coils during an operating scenario experiences out-of-plane forces caused by the interaction between the 68kA operating TF current and the poloidal magnetic fields. In order to keep the induced static and cyclic stress range in the intercoil shear keys between coils cases within the ITER allowable limits [1], centripetal preload is introduced by means of S2 fiber-glass/epoxy composite pre-compression rings (PCRs). Those PCRs consist in two sets of three rings, each 5 m in diameter and 337 × 288 mm in cross-section, and are installed at the top and bottom regions to apply a total resultant preload of 70 MN per TF coil equivalent to about 400 MPa hoop stress. Recent developments of composites in the aerospace industry have accelerated the use of advanced composites as primary structural materials. The PCRs represent one of the most challenging composite applications of large dimensions and highly stressed structures operating at 4 K over a long term life. Efficient design of those pre-compression composite structures requires a detailed understanding of both the failure behavior of the structure and the fracture behavior of the material. Due to the inherent difficulties to carry out real scale testing campaign, there is a need to develop simulation tools to predict the multiple complex failure mechanisms in pre-compression rings. A framework contract was placed by ITER Organization with SENER Ingenieria y Sistemas SA to develop multi-scale models representative of the composite structure of the Pre-compression rings based on experimental material data. The predictive modeling based on ABAQUS FEM provides the opportunity both to understand better how PCR composites behave in operating conditions and to support the development of materials by the supplier with enhanced performance to withstand the machine design lifetime of 30,000 cycles. The multi-scale stress analysis has revealed a complete picture of the stress levels within the fiber and the matrix regarding the static and fatigue performance of the rings structure including the presence of a delamination defect of critical size. The analysis results of the composite material demonstrate that the rings performance objectives under all loading and strength conditions are met.

An active homopolar magnetic bearing with high temperature superconductor (HTS) coils and ferromagnetic cores

NASA Technical Reports Server (NTRS)

Brown, G. V.; Dirusso, E.; Provenza, A. J.

1995-01-01

A proof-of-feasibility demonstration showed that high temperature superconductor (HTS) coils can be used in a high-load, active magnetic bearing in liquid nitrogen. A homopolar radial bearing with commercially wound HTS (Bi 2223) bias and control coils produced over 200 lb (890 N) radial load capacity (measured non-rotating) and supported a shaft to 14000 rpm. The goal was to show that HTS coils can operate stably with ferromagnetic cores in a feedback controlled system at a current density similar to that in Cu in liquid nitrogen. Design compromises permitted use of circular coils with rectangular cross section. Conductor improvements will eventually permit coil shape optimization, higher current density and higher bearing load capacity. The bias coil, wound with non-twisted, multifilament HTS conductor, required negligible power to carry its direct current. The control coils were wound with monofilament HTS sheathed in Ag. These dissipated negligible power for direct current (i.e. for steady radial load components). When an alternating current (AC) was added, the AC component dissipated power which increased rapidly with frequency and quadratically with AC amplitude. In fact at frequencies above about 2 hz, the effective resistance of the control coil conductor actually exceeds that of the silver which is in electrical parallel with the oxide superconductor. This is at least qualitatively understandable in the context of a Bean-type model of flux and current penetration into a Type II superconductor. Fortunately the dynamic currents required for bearing stability are of small amplitude. These results show that while twisted multifilament conductor is not needed for stable levitation, twisted multifilaments will be required to reduce control power for sizable dynamic loads, such as those due to unbalance.

A double-helix and cross-patterned solenoid used as a wirelessly powered receiver for medical implants

NASA Astrophysics Data System (ADS)

Mao, Shitong; Wang, Hao; Mao, Zhi-Hong; Sun, Mingui

2018-05-01

Many medical implants need to be designed in the shape of a cylinder (rod), a cuboid or a capsule in order to adapt to a specific site within the human body or facilitate the implantation procedure. In order to wirelessly power these types of implants, a pair of coils, one is located inside the human body and one is outside, is often used. Since most organs such as major muscles, blood vessels, and nerve bundles are anatomically parallel to the body surface, the most desired wireless power transfer (WPT) direction is from the external power transmission pad (a planar coil) to the lateral surface of the implant. However, to obtain optimal coupling, the currently used solenoid coil requires being positioned perpendicular to the body surface, which is often medically or anatomically unacceptable. In this research, a concentric double-helix (DH) coil with an air core is presented for use in implantable devices. Two helical coils are tilted at opposite angles (±45 degrees) to form a cross pattern. The WPT system is designed using the magnetic resonance concept for wireless power transfer (MR-WPT). The power transfer efficiency (PTE) relies on the near-field magnetic coupling which is closely related to the location and orientation of the DH coil. We explain how the novel structure of the DH solenoid magnifies the mutual inductance with the widely adopted circular planner coil and how the PTE is improved in comparison to the case of the conventional solenoid coil. We also study an important case where the double-helix power reception coil is laterally and angularly misaligned with the transmitter. Finally, our computational study using the finite element method and experimental study with actually constructed prototypes are presented which have proven our new double-helix coil design.

The significant impact of framing coils on long-term outcomes in endovascular coiling for intracranial aneurysms: how to select an appropriate framing coil.

PubMed

Ishida, Wataru; Sato, Masayuki; Amano, Tatsuo; Matsumaru, Yuji

2016-09-01

OBJECTIVE The importance of a framing coil (FC)-the first coil inserted into an aneurysm during endovascular coiling, also called a lead coil or a first coil-is recognized, but its impact on long-term outcomes, including recanalization and retreatment, is not well established. The purposes of this study were to test the hypothesis that the FC is a significant factor for aneurysmal recurrence and to provide some insights on appropriate FC selection. METHODS The authors retrospectively reviewed endovascular coiling for 280 unruptured intracranial aneurysms and gathered data on age, sex, aneurysm location, aneurysm morphology, maximal size, neck width, adjunctive techniques, recanalization, retreatment, follow-up periods, total volume packing density (VPD), volume packing density of the FC, and framing coil percentage (FCP; the percentage of FC volume in total coil volume) to clarify the associated factors for aneurysmal recurrence. RESULTS Of 236 aneurysms included in this study, 33 (14.0%) had recanalization, and 18 (7.6%) needed retreatment during a mean follow-up period of 37.7 ± 16.1 months. In multivariate analysis, aneurysm size (odds ratio [OR] = 1.29, p < 0.001), FCP < 32% (OR 3.54, p = 0.009), and VPD < 25% (OR 2.96, p = 0.015) were significantly associated with recanalization, while aneurysm size (OR 1.25, p < 0.001) and FCP < 32% (OR 6.91, p = 0.017) were significant predictors of retreatment. VPD as a continuous value or VPD with any cutoff value could not predict retreatment with statistical significance in multivariate analysis. CONCLUSIONS FCP, which is equal to the FC volume as a percentage of the total coil volume and is unaffected by the morphology of the aneurysm or the measurement error in aneurysm length, width, or height, is a novel predictor of recanalization and retreatment and is more significantly predictive of retreatment than VPD. To select FCs large enough to meet the condition of FCP ≥ 32% is a potential relevant factor for better long-term outcomes. These findings support our hypothesis that the FC is a significant factor for aneurysmal recurrence.

Retreatment of recanalized aneurysms after Y-stent-assisted coil embolization with double enterprise stents: case report and systematic review of the literature.

PubMed

Kono, Kenichi; Shintani, Aki; Terada, Tomoaki

2014-01-01

It is necessary to consider possibility of recanalization and retreatment after coil embolization for cerebral aneurysms. There is concern that retreatment for recanalized aneurysms after Y-stent-assisted coil embolization may be difficult because of double stents, especially in Y-stents with double closed-cell stents owing to narrowed structures. However, no detailed reports of retreatment after Y-stent have been reported. Between July 2010 and June 2013, we treated four aneurysms with Y-stent-assisted coil embolization using Enterprise closed-cell stents. Recanalization occurred in one case (25%), and retreatment was performed. We easily navigated a microcatheter into the target portions of the aneurysm through the Y-stent and occluded the aneurysm with coils. Additionally, by systematically searching in PubMed, we found 105 cases of Y-stent-assisted coil embolization using Enterprise stents or Neuroform stents with more than 6 months of follow-up. Among them, retreatment was performed in 10 cases (9.5%). There were no significant differences in retreatment rates among different stent combinations (P=0.91; Fisher's exact test). In conclusion, navigation of a microcatheter into the aneurysm through the Y-stent with double Enterprise stents was feasible, and retreatment rates after Y-stent-assisted coiling may not depend on stent combinations.

NMR of thin layers using a meanderline surface coil

DOEpatents

Cowgill, Donald F.

2001-01-01

A miniature meanderline sensor coil which extends the capabilities of nuclear magnetic resonance (NMR) to provide analysis of thin planar samples and surface layer geometries. The sensor coil allows standard NMR techniques to be used to examine thin planar (or curved) layers, extending NMRs utility to many problems of modern interest. This technique can be used to examine contact layers, non-destructively depth profile into films, or image multiple layers in a 3-dimensional sense. It lends itself to high resolution NMR techniques of magic angle spinning and thus can be used to examine the bonding and electronic structure in layered materials or to observe the chemistry associated with aging coatings. Coupling this sensor coil technology with an arrangement of small magnets will produce a penetrator probe for remote in-situ chemical analysis of groundwater or contaminant sediments. Alternatively, the sensor coil can be further miniaturized to provide sub-micron depth resolution within thin films or to orthoscopically examine living tissue. This thin-layer NMR technique using a stationary meanderline coil in a series-resonant circuit has been demonstrated and it has been determined that the flat meanderline geometry has about he same detection sensitivity as a solenoidal coil, but is specifically tailored to examine planar material layers, while avoiding signals from the bulk.

Superconducting Electromagnetic Suspension (EMS) system for Grumman Maglev concept

NASA Technical Reports Server (NTRS)

Kalsi, Swarn S.

1994-01-01

The Grumman developed Electromagnetic Suspension (EMS) Maglev system has the following key characteristics: a large operating airgap--40 mm; levitation at all speeds; both high speed and low speed applications; no deleterious effects on SC coils at low vehicle speeds; low magnetic field at the SC coil--less than 0.35 T; no need to use non-magnetic/non-metallic rebar in the guideway structure; low magnetic field in passenger cabin--approximately 1 G; low forces on the SC coil; employs state-of-the-art NbTi wire; no need for an active magnet quench protection system; and lower weight than a magnet system with copper coils. The EMS Maglev described in this paper does not require development of any new technologies. The system could be built with the existing SC magnet technology.

Wireless power-receiving assembly for a telemetry system in a high-temperature environment of a combustion turbine engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bevly, III, Alex J.; McConkey, Joshua S.

In a telemetry system (100) in a high-temperature environment of a combustion turbine engine (10), a wireless power-receiving coil assembly (116) may be affixed to a movable component (104) of the turbine engine. Power-receiving coil assembly (116) may include a radio-frequency transparent housing (130) having an opening (132). A lid (134) may be provided to close the opening of the housing. Lid (134) may be positioned to provide support against a surface (120) of the movable component. An induction coil (133) is disposed in the housing distally away from the lid and encased between a first layer (136) and amore » last layer (140) of a potting adhesive. Lid (134) is arranged to provide vibrational buffering between the surface (120) of the movable component (104) and the layers encasing the induction coil.« less

Acute lung injury following refrigeration coil deicing.

PubMed

McKeown, Nathanael J; Burton, Brent T

2012-03-01

We report a case of a worker who developed ALI requiring mechanical ventilatory support after attempting to melt ice condensate by applying the flame of an oxy-acetylene torch to refrigeration coils charged with a halocarbon refrigerant in a closed environment. A discussion of possible etiologies are discussed, including phosgene, carbonyl fluoride, and nitrogen oxides. Primary prevention with adequate respiratory protection is recommended whenever deicing is performed in a closed space environment.

Characteristics of the Footprints of Field Lines for Variable Location of Plate for a Single-Null Divertor Tokamak with the Effects of Dipole Coil Using Method of Maps

NASA Astrophysics Data System (ADS)

Burton, Joni; Ali, Halima; Punjabi, Alkesh

1996-11-01

We determine the properties of the footprint of the magnetic field lines from the stochastic scrape-off layer of a single-null divertor tokamak including the effects of an externally placed dipole coil as the location of the divertor plate is varied. We use the Method of Maps (Punjabi A, Verma A and Boozer A, Phys Rev Lett), 69, 3322 (1992) and J Plasma Phys, 52, 91 (1994) for this investigation. The unperturbed magnetic topology is represented by the Symmetric Simple Map (Ali H, Watson M, Mayer C, Punjabi A and Boozer A, Bull Am Phys Soc), 40, 1855 (1995). The effects of the dipole coil are repesented by the Dipole Map (Ali H, Watson M, Punjabi A and Boozer A, Sherwood Mtg), paper 1C20 (1996). A single dipole coil is placed across from the X-point below the last good surface. The area of the footprint is calculated using the method of fractal dimesion. This work is supported by US DOE OFES. Joni Burton is an undergraduate mathematics major at Hampton University. She is a Ronald E. McNair Scholar at HU supported by R. E. McNair Foundation.

Characterization of a custom-built RF coil for a high-resolution phase-contrast magnetic resonance velocimeter

NASA Astrophysics Data System (ADS)

Yang, Byungkuen; Cho, Jee-Hyun; Song, Simon

2016-11-01

For the use of clinical purpose magnetic resonance velocimeter (MRV) is a versatile flow visualization technique in that it allows opaque flow, complex geometry, no use of tracer particles and facile fast non-invasive measurements of 3 dimensional and 3 component velocity vectors. However, the spatial resolution of a commercial MR machine is lower than optics-based techniques like PIV. On the other hand, the use of MRV for clinical purposes like cardiovascular flow visualization requires accurate measurements or estimations on wall shear stress (WSS) with a high spatial resolution. We developed a custom-built solenoid RF coil for phase-contrast (PC) MRV to improve its resolution. We compared signal-to-noise ratio, WSS estimations, partial volume effects near wall between the custom RF coil and a commercial coil. Also, a Hagen-Poiseuille flow was analyzed with the custom RF coil. This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP) (No. 2016R1A2B3009541).

A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis.

PubMed

Guo, Qinglan; Weng, Jingwei; Xu, Xiaogang; Wang, Minghua; Wang, Xiaoying; Ye, Xinyu; Wang, Wenning; Wang, Minggui

2010-10-08

The first report on the transferable, plasmid-mediated quinolone-resistance determinant qnrA1 was in 1998. Since then, qnr alleles have been discovered worldwide in clinical strains of Gram-negative bacilli. Qnr proteins confer quinolone resistance, and belong to the pentapeptide repeat protein (PRP) family. Several PRP crystal structures have been solved, but little is known about the functional significance of their structural arrangement. We conducted random and site-directed mutagenesis on qnrA1 and on qnrC, a newly identified quinolone-resistance gene from Proteus mirabilis. Many of the Qnr mutants lost their quinolone resistance function. The highly conserved hydrophobic Leu or Phe residues at the center of the pentapeptide repeats are known as i sites, and loss-of-function mutations included replacement of the i site hydrophobic residues with charged residues, replacing the i-2 site, N-terminal to the i residues, with bulky side-chain residues, introducing Pro into the β-helix coil, deletion of the N- and C-termini, and excision of a central coil. Molecular dynamics simulations and homology modeling demonstrated that QnrC overall adopts a stable β-helix fold and shares more similarities with MfpA than with other PRP structures. Based on homology modeling and molecular dynamics simulation, the dysfunctional point mutations introduced structural deformations into the quadrilateral β-helix structure of PRPs. Of the pentapeptides of QnrC, two-thirds adopted a type II β-turn, while the rest adopted type IV turns. A gap exists between coil 2 and coil 3 in the QnrC model structure, introducing a structural flexibility that is similar to that seen in MfpA. The hydrophobic core and the β-helix backbone conformation are important for maintaining the quinolone resistance property of Qnr proteins. QnrC may share structural similarity with MfpA.

Experiment study on an inductive superconducting fault current limiter using no-insulation coils

NASA Astrophysics Data System (ADS)

Qiu, D.; Li, Z. Y.; Gu, F.; Huang, Z.; Zhao, A.; Hu, D.; Wei, B. G.; Huang, H.; Hong, Z.; Ryu, K.; Jin, Z.

2018-03-01

No-insulation (NI) coil made of 2 G high temperature superconducting (HTS) tapes has been widely used in DC magnet due to its excellent performance of engineering current density, thermal stability and mechanical strength. However, there are few AC power device using NI coil at present. In this paper, the NI coil is firstly applied into inductive superconducting fault current limiter (iSFCL). A two-winding structure air-core iSFCL prototype was fabricated, composed of a primary copper winding and a secondary no-insulation winding using 2 G HTS coated conductors. Firstly, in order to testify the feasibility to use NI coil as the secondary winding, the impedance variation of the prototype at different currents and different cycles was tested. The result shows that the impedance increases rapidly with the current rises. Then the iSFCL prototype was tested in a 40 V rms/ 3.3 kA peak short circuit experiment platform, both of the fault current limiting and recovery property of the iSFCL are discussed.

SU-E-J-239: Influence of RF Coil Materials On Surface and Buildup Dose From a 6MV Photon Beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghila, A; Fallone, B; Rathee, S

2015-06-15

Purpose: In order to perform real time tumour tracking using an integrated Linac-MR, images have to be acquired during irradiation. MRI uses RF coils in close proximity to the imaged volume. Given current RF coil designs this means that the high energy photons will be passing through the coil before reaching the patient. This study experimentally investigates the dose modifications that occur due to the presence of various RF coil materials in the treatment beam. Methods: Polycarbonate, copper or aluminum tape, and Teflon were used to emulate the base, conductor and cover respectively of a surface RF coil. These materialsmore » were placed at various distances from the surface of polystyrene or solid water phantoms which were irradiated in the presence of no magnetic field, a transverse 0.2T magnetic field, and a parallel 0.2T magnetic field. Percent depth doses were measured using ion chambers. Results: A significant increase in surface and buildup dose is observed. The surface dose is seen to decrease with an increasing separation between the emulated coil and the phantom surface, when no magnetic field is present. When a transverse magnetic field is applied the surface dose decreases faster with increasing separation, as some of the electrons created in the coil are curved away from the phantom’s surface. When a parallel field is present the surface dose stays approximately constant for small separations, only slightly decreasing for separations greater than 5cm, since the magnetic field focuses the electrons produced in the coil materials not allowing them to scatter. Conclusion: Irradiating a patient through an RF coil leads to an increase in the surface and buildup doses. Mitigating this increase is important for the successful clinical use of either a transverse or a parallel configuration Linac-MR unit. This project is partially supported by an operating grant from the Canadian Institute of Health Research (CIHR MOP 93752)« less

A Two-dimensional Sixteen Channel Transmit/Receive Coil Array for Cardiac MRI at 7.0 Tesla: Design, Evaluation and Application

PubMed Central

Thalhammer, Christof; Renz, Wolfgang; Winter, Lukas; Hezel, Fabian; Rieger, Jan; Pfeiffer, Harald; Graessl, Andreas; Seifert, Frank; Hoffmann, Werner; von Knobelsdorff-Brenkenhoff, Florian; Tkachenko, Valeriy; Schulz-Menger, Jeanette; Kellman, Peter; Niendorf, Thoralf

2012-01-01

Purpose To design, evaluate and apply a two-dimensional 16 channel transmit/receive coil array tailored for cardiac MRI at 7.0 Tesla. Material and Methods The cardiac coil array consists of 2 sections each using 8 elements arranged in a 2 × 4 array. RF safety was validated by SAR simulations. Cardiac imaging was performed using 2D CINE FLASH imaging, T2* mapping and fat-water separation imaging. The characteristics of the coil array were analyzed including parallel imaging performance, left ventricular chamber quantification and overall image quality. Results RF characteristics were found to be appropriate for all subjects included in the study. The SAR values derived from the simulations fall well in the limits of legal guidelines. The baseline SNR advantage at 7.0 T was put to use to acquire 2D CINE images of the heart with a very high spatial resolution of (1 × 1 × 4) mm3. The proposed coil array supports 1D acceleration factors of up to R=4 without impairing image quality significantly. Conclusions The 16 channel TX/RX coil has the capability to acquire high contrast and high spatial resolution images of the heart at 7.0 Tesla. PMID:22706727

Apparatus and process for making a superconducting magnet for particle accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jarabak, A.J.; Sunderman, W.H.; Mendola, E.G.

1992-03-10

This patent describes an apparatus for manufacturing a coil of superconducting material. It comprises a horizontally disposed winding mandrel; an adjustable support for receiving a spool of superconducting material, the spool having a vertical axis; means for translating the spool of superconducting material in a generally oval path around the winding mandrel so that the superconducting material is de-reeled from the spool, in order to wind a predetermined amount of superconducting material onto the mandrel, such that a coil of superconducting material is formed; means for guiding the superconducting material from the spool so as to deliver the superconducting materialmore » to the winding mandrel on a plane perpendicular to the vertical axis of the spool and parallel with a winding plane on the winding mandrel; means for imparting a tensioning force on the superconducting material as it is guided from the spool; means for rotating the winding mandrel about the horizontal axis thereof; means for clamping the superconducting material against the winding mandrel as the wire is wound thereon; means for securing the coil to the winding mandrel for lifting mandrel with the coil thereon; and means for curing the coil of superconducting material whereby a finished coil of superconducting material is formed.« less

Anatomical and metabolic assessment of prostate using a 3-Tesla MR scanner with a custom-made external transceive coil: healthy volunteer study.

PubMed

Kaji, Yasushi; Kuroda, Kagayaki; Maeda, Takaki; Kitamura, Yuri; Fujiwara, Toshitaka; Matsuoka, Yuichiro; Tamura, Mitsuru; Takei, Naoyuki; Matsuda, Tsuyoshi; Sugimura, Kazuro

2007-03-01

To examine the possibility of using a 3 Tesla (T) magnetic resonance (MR) scanner with a custom-made external coil to obtain ductal details of the prostate, high-quality spectra, and metabolite mapping corresponding to prostate zonal anatomy in healthy volunteers. MRI and two-dimensional (2D) chemical shift imaging (CSI) were performed in 16 healthy volunteers using a 3T scanner with a custom-made external transmit-receive (transceive) coil. Visualization of the prostatic duct-like structure was analyzed on T2-weighted (T2W) images. The resolution of the metabolite peaks and the distribution of metabolites in CSI were also assessed. In the axial plane, 3-mm-thick images were better than 4-mm-thick images with the same voxel volume for assessing duct-like structures and prostatic urethra. Differentiation between inner and outer citrate (Cit) peaks was frequently observed (29 out of 30). The mean peak area ratio of choline (Cho) plus creatine (Cr) over Cit in the peripheral zone (PZ) was significantly lower than in the transition zone (TZ) (P = 0.014). 3T MR examinations of the prostate using an external coil allow information to be collected about the details of duct-like structures, the high-quality spectra of Cit, and the zone-specific distribution of metabolites.

Modeling and Evaluation of Canted Coil Springs as High Temperature Seal Preloading Devices

NASA Technical Reports Server (NTRS)

Oswald, Jay J.; Mullen, Robert L.; Dunlap, Patrick H., Jr.; Steinetz, Bruce M.

2004-01-01

Future reusable launch vehicles will require advanced structural seals. This includes propulsion seals along edges and hinge lines in hypersonic engines, and control surface seals for movable flaps and elevons on proposed reentry vehicles. Seals must remain in sealing engagement with opposing surfaces, for multiple missions, even though the seal gap may be opening and closing due to thermal and structural loads. To meet this requirement either the seals themselves must be resilient or there must be a resilient structural element behind the seals. Case Western Reserve University is working with NASA s Glenn Research Center to develop more resilient high temperature seal components and preloading devices. Results are presented for a finite element analysis of a canted coil spring that is being considered as a high temperature seal preloading device. This type of spring is a leading candidate due to its ability to provide nearly constant force over a large deflection. The finite element analyses were verified by comparing them to experimental results of canted coil springs of three different stiffnesses, measured at Glenn Research Center. Once validated the parameterized model was combined with a scripting algorithm to assess the effects of key spring design variables (wire diameter, coils per inch, cant amplitude, eccentricity, and spring width) on spring stiffness and maximum Von Mises stress to aid in subsequent design.

Method and apparatus for the formation of a spheromak plasma

DOEpatents

Yamada, Masaaki; Furth, Harold P.; Stix, Thomas H.; Todd, Alan M. M.

1982-01-01

A method and apparatus for forming a detached, compact toroidally shaped spheromak plasma by an inductive mechanism. A generally spheroidal vacuum vessel (1) houses a toroidally shaped flux ring or core (2) which contains poloidal and toroidal field generating coils. A plasma discharge occurs with the pulsing of the toroidal field coil, and the plasma is caused to expand away from the core (2) and toward the center of the vacuum vessel (1). When the plasma is in an expanded state, a portion of it is pinched off in order to form a separate, detached spheromak plasma configuration. The detached plasma is supported by a magnetic field generated by externally arranged equilibrium field coils (5).

Effects of Hesel-coil deep transcranial magnetic stimulation for depression - a systematic review.

PubMed

Nordenskjöld, Axel; Mårtensson, Björn; Pettersson, Agneta; Heintz, Emelie; Landén, Mikael

2016-10-01

One third of the depressed patients are not improved by antidepressant drugs and psychological treatments, and there is a need for additional treatments. Repetitive transcranial magnetic stimulation (rTMS) is being developed towards an alternative in treatment-resistant depression. Deep transcranial stimulation (dTMS) with the Hesel-coil (H-coil) is a further development of rTMS aiming to enhance the effect by getting the magnetic pulses to penetrate deeper into the brain. This report aims to assess the evidence-base for dTMS for depression. The report also includes an assessment of the ethical and economic aspects involved. A systematic review of the effects of H-coil dTMS on depression was conducted and the scientific support was evaluated using GRADE (Grading of Recommendations Assessment, Development and Evaluation). Only one controlled study was identified. In the sham-controlled randomized study, 212 participants with major depression that had not responded to antidepressant medication were enrolled. A two-point superiority in Hamilton Depression Rating Scale was observed in the dTMS arm vs the sham-arm at 4 weeks, but the difference was not statistically significant. No serious adverse events were reported apart from rare cases of epileptic seizures. The existing scientific support for H-coil dTMS therapy for depression is insufficient. The clinical implication is that the use of dTMS in depression should be restricted to the framework of clinical trials pending further studies. Fortunately, additional studies are underway and the evidence base should presumably improve over the next several years.

Effects of Hesel-coil deep transcranial magnetic stimulation for depression – a systematic review

PubMed Central

Nordenskjöld, Axel; Mårtensson, Björn; Pettersson, Agneta; Heintz, Emelie; Landén, Mikael

2016-01-01

Abstract Background: One third of the depressed patients are not improved by antidepressant drugs and psychological treatments, and there is a need for additional treatments. Repetitive transcranial magnetic stimulation (rTMS) is being developed towards an alternative in treatment-resistant depression. Deep transcranial stimulation (dTMS) with the Hesel-coil (H-coil) is a further development of rTMS aiming to enhance the effect by getting the magnetic pulses to penetrate deeper into the brain. Aims: This report aims to assess the evidence-base for dTMS for depression. The report also includes an assessment of the ethical and economic aspects involved. Methods: A systematic review of the effects of H-coil dTMS on depression was conducted and the scientific support was evaluated using GRADE (Grading of Recommendations Assessment, Development and Evaluation). Results: Only one controlled study was identified. In the sham-controlled randomized study, 212 participants with major depression that had not responded to antidepressant medication were enrolled. A two-point superiority in Hamilton Depression Rating Scale was observed in the dTMS arm vs the sham-arm at 4 weeks, but the difference was not statistically significant. No serious adverse events were reported apart from rare cases of epileptic seizures. Conclusions: The existing scientific support for H-coil dTMS therapy for depression is insufficient. The clinical implication is that the use of dTMS in depression should be restricted to the framework of clinical trials pending further studies. Fortunately, additional studies are underway and the evidence base should presumably improve over the next several years. PMID:27093104

Assembly Tests of the First Nb 3 Sn Low-Beta Quadrupole Short Model for the Hi-Lumi LHC

DOE PAGES

Pan, H.; Felice, H.; Cheng, D. W.; ...

2016-01-18

In preparation for the high-luminosity upgrade of the Large Hadron Collider (LHC), the LHC Accelerator Research Program (LARP) in collaboration with CERN is pursuing the development of MQXF: a 150-mm-aperture high-field Nb3Sn quadrupole magnet. Moreover, the development phase starts with the fabrication and test of several short models (1.2-m magnetic length) and will continue with the development of several long prototypes. All of them are mechanically supported using a shell-based support structure, which has been extensively demonstrated on several R&D models within LARP. The first short model MQXFS-AT has been assembled at LBNL with coils fabricated by LARP and CERN.more » In our paper, we summarize the assembly process and show how it relies strongly on experience acquired during the LARP 120-mm-aperture HQ magnet series. We also present comparison between strain gauges data and finite-element model analysis. Finally, we present the implication of the MQXFS-AT experience on the design of the long prototype support structure.« less

Investigation of the B1 field distribution and RF power deposition in a birdcage coil as functions of the number of coil legs at 4.7 T, 7.0 T, and 11.7 T

NASA Astrophysics Data System (ADS)

Seo, Jeung-Hoon; Han, Sang-Doc; Kim, Kyoung-Nam

2015-06-01

The proper design of birdcage (BC) coils plays a very important role in the acquisition of highresolution magnetic resonance imaging (MRI) of small animals such as rodents. In this context, we investigate multiple-leg (8-, 16-, 32-, 64-, and 128-leg) BC coils operating at ultra-high fields (UHF) of 7.0 T and 11.7 T and a high-field (HF) of 4.7 T for rodent magnetic resonance imaging (MRI). Primarily, Our study comparatively examines the parameters of the radiofrequency (RF) transmission (|B1 +|)-field, the magnetic flux (|B1|)-field, and RF power deposition (RF-PD) as functions of the number of BC-coil legs via finite-difference time-domain (FDTD) calculations under realistic loading conditions with a biological phantom. In particular, the specific ratio |E/B1 +| is defined for predicting RF-PD values in different coil structures. Our results indicate that the optimal number of legs of the BC coil can be chosen for different resonance frequencies of 200 MHz, 300 MHz, and 500 MHz and that this choice can be lead to superior |B1 +|-field intensity and |B1|-field homogeneity and decreased RF-PD. We believe that our approach to determining the optimal number of legs for a BC coil can contribute to rodent MR imaging.

All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.

PubMed Central

Guo, Y; Bozic, D; Malashkevich, V N; Kammerer, R A; Schulthess, T; Engel, J

1998-01-01

The potential storage and delivery function of cartilage oligomeric matrix protein (COMP) for cell signaling molecules was explored by binding hydrophobic compounds to the recombinant five-stranded coiled-coil domain of COMP. Complex formation with benzene, cyclohexane, vitamin D3 and elaidic acid was demonstrated through increases in denaturation temperatures of 2-10 degreesC. For all-trans retinol and all-trans retinoic acid, an equilibrium dissociation constant KD = 0.6 microM was evaluated by fluorescence titration. Binding of benzene and all-trans retinol into the hydrophobic axial pore of the COMP coiled-coil domain was proven by the X-ray crystal structures of the corresponding complexes at 0.25 and 0.27 nm resolution, respectively. Benzene binds with its plane perpendicular to the pore axis. The binding site is between the two internal rings formed by Leu37 and Thr40 pointing into the pore of the COMP coiled-coil domain. The retinol beta-ionone ring is positioned in a hydrophobic environment near Thr40, and the 1.1 nm long isoprene tail follows a completely hydrophobic region of the pore. Its terminal hydroxyl group complexes with a ring of the five side chains of Gln54. A mutant in which Gln54 is replaced by Ile binds all-trans retinol with affinity similar to the wild-type, demonstrating that hydrophobic interactions are predominant. PMID:9736606

Boehringer Mannheim award lecture 1995. La conference Boehringer Mannheim 1995. De novo design of alpha-helical proteins: basic research to medical applications.

PubMed

Hodges, R S

1996-01-01

The two-stranded alpha-helical coiled-coil is a universal dimerization domain used by nature in a diverse group of proteins. The simplicity of the coiled-coil structure makes it an ideal model system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design. The issues that must be addressed in the de novo design of coiled-coils for use in research and medical applications are (i) controlling parallel versus antiparallel orientation of the polypeptide chains, (ii) controlling the number of helical strands in the assembly (iii) maximizing stability of homodimers or heterodimers in the shortest possible chain length that may require the engineering of covalent constraints, and (iv) the ability to have selective heterodimerization without homodimerization, which requires a balancing of selectivity versus affinity of the dimerization strands. Examples of our initial inroads in using this de novo design motif in various applications include: heterodimer technology for the detection and purification of recombinant peptides and proteins; a universal dimerization domain for biosensors; a two-stage targeting and delivery system; and coiled-coils as templates for combinatorial helical libraries for basic research and drug discovery and as synthetic carrier molecules. The universality of this dimerization motif in nature suggests an endless number of possibilities for its use in de novo design, limited only by the creativity of peptide-protein engineers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Yirui; Scheuermann, Thomas H.; Partch, Carrie L.

The hypoxia-inducible factor complex (HIF-α·aryl hydrocarbon receptor nuclear translocator (ARNT)) requires association with several transcription coactivators for a successful cellular response to hypoxic stress. In addition to the conventional global transcription coactivator CREB-binding protein/p300 (CBP/p300) that binds to the HIF-α transactivation domain, a new group of transcription coactivators called the coiled-coil coactivators (CCCs) interact directly with the second PER-ARNT-SIM (PAS) domain of ARNT (ARNT PAS-B). These less studied transcription coactivators play essential roles in the HIF-dependent hypoxia response, and CCC misregulation is associated with several forms of cancer. To better understand CCC protein recruitment by the heterodimeric HIF transcription factor,more » we used x-ray crystallography, NMR spectroscopy, and biochemical methods to investigate the structure of the ARNT PAS-B domain in complex with the C-terminal fragment of a coiled-coil coactivator protein, transforming acidic coiled-coil coactivator 3 (TACC3). We found that the HIF-2α PAS-B domain also directly interacts with TACC3, motivating an NMR data-derived model suggesting a means by which TACC3 could form a ternary complex with HIF-2α PAS-B and ARNT PAS-B via β-sheet/coiled-coil interactions. Furthermore, these findings suggest that TACC3 could be recruited as a bridge to cooperatively mediate between the HIF-2α PAS-B·ARNT PAS-B complex, thereby participating more directly in HIF-dependent gene transcription than previously anticipated.« less

Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up.

PubMed

Hong, Jing; Kharenko, Olesya A; Ogawa, Michael Y

2006-12-11

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.

Dynamic control of laser driven proton beams by exploiting self-generated, ultrashort electromagnetic pulses

NASA Astrophysics Data System (ADS)

Kar, S.; Ahmed, H.; Nersisyan, G.; Brauckmann, S.; Hanton, F.; Giesecke, A. L.; Naughton, K.; Willi, O.; Lewis, C. L. S.; Borghesi, M.

2016-05-01

As part of the ultrafast charge dynamics initiated by high intensity laser irradiations of solid targets, high amplitude EM pulses propagate away from the interaction point and are transported along any stalks and wires attached to the target. The propagation of these high amplitude pulses along a thin wire connected to a laser irradiated target was diagnosed via the proton radiography technique, measuring a pulse duration of ˜20 ps and a pulse velocity close to the speed of light. The strong electric field associated with the EM pulse can be exploited for controlling dynamically the proton beams produced from a laser-driven source. Chromatic divergence control of broadband laser driven protons (upto 75% reduction in divergence of >5 MeV protons) was obtained by winding the supporting wire around the proton beam axis to create a helical coil structure. In addition to providing focussing and energy selection, the technique has the potential to post-accelerate the transiting protons by the longitudinal component of the curved electric field lines produced by the helical coil lens.

Dynamic control of laser driven proton beams by exploiting self-generated, ultrashort electromagnetic pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kar, S., E-mail: s.kar@qub.ac.uk; Ahmed, H.; Nersisyan, G.

As part of the ultrafast charge dynamics initiated by high intensity laser irradiations of solid targets, high amplitude EM pulses propagate away from the interaction point and are transported along any stalks and wires attached to the target. The propagation of these high amplitude pulses along a thin wire connected to a laser irradiated target was diagnosed via the proton radiography technique, measuring a pulse duration of ∼20 ps and a pulse velocity close to the speed of light. The strong electric field associated with the EM pulse can be exploited for controlling dynamically the proton beams produced from amore » laser-driven source. Chromatic divergence control of broadband laser driven protons (upto 75% reduction in divergence of >5 MeV protons) was obtained by winding the supporting wire around the proton beam axis to create a helical coil structure. In addition to providing focussing and energy selection, the technique has the potential to post-accelerate the transiting protons by the longitudinal component of the curved electric field lines produced by the helical coil lens.« less

Two mannose-binding lectin homologues and an MBL-associated serine protease are expressed in the gut epithelia of the urochordate species Ciona intestinalis.

PubMed

Skjoedt, Mikkel-Ole; Palarasah, Yaseelan; Rasmussen, Karina; Vitved, Lars; Salomonsen, Jan; Kliem, Anette; Hansen, Soren; Koch, Claus; Skjodt, Karsten

2010-01-01

The lectin complement pathway has important functions in vertebrate host defence and accumulating evidence of primordial complement components trace its emergence to invertebrate phyla. We introduce two putative mannose-binding lectin homologues (CioMBLs) from the urochordate species Ciona intestinalis. The CioMBLs display similarities with vertebrate MBLs and comprise a collagen-like region, alpha-helical coiled-coils and a carbohydrate recognition domain (CRD) with conserved residues involved in calcium and carbohydrate binding. Structural analysis revealed an oligomerization through interchain disulphide bridges between N-terminal cysteine residues and cysteines located between the neck region and the CRD. RT-PCR showed a tissue specific expression of CioMBL in the gut and by immunohistochemistry analysis we also demonstrated that CioMBL co-localize with an MBL-associated serine protease in the epithelia cells lining the stomach and intestine. In conclusion we present two urochordate MBLs and identify an associated serine protease, which support the concept of an evolutionary ancient origin of the lectin complement pathway.

Magnetic sensor for building structural vibrations.

PubMed

García, Alfonso; Morón, Carlos; Tremps, Enrique

2014-02-05

This paper shows a new displacement-to-frequency transducer based on the variation of a coil inductance when a magnetic core is partially or completely inserted inside. This transducer is based on a Colpitts oscillator due its low manufacturing price, behavior and immunity to noise. A tank circuit with a configuration in parallel was used because it can be employed at lower frequencies and it enables it to make a direct analysis. The sensor has a dynamic range equal to the length of the coil. The cores can exchange sensors (coils with its ferromagnetic core) using the same electronic measuring system. In this way, with only an electronic circuit, the core sensor determines the measurement range. The obtained resolution is higher than 1/100,000, and the sensor also allows the measurement and knowing in real time the effect of vibration, thermal expansion, referred overload movements, etc.., that can occur in the structural elements of a building.

Vision-based surface defect inspection for thick steel plates

NASA Astrophysics Data System (ADS)

Yun, Jong Pil; Kim, Dongseob; Kim, KyuHwan; Lee, Sang Jun; Park, Chang Hyun; Kim, Sang Woo

2017-05-01

There are several types of steel products, such as wire rods, cold-rolled coils, hot-rolled coils, thick plates, and electrical sheets. Surface stains on cold-rolled coils are considered defects. However, surface stains on thick plates are not considered defects. A conventional optical structure is composed of a camera and lighting module. A defect inspection system that uses a dual lighting structure to distinguish uneven defects and color changes by surface noise is proposed. In addition, an image processing algorithm that can be used to detect defects is presented in this paper. The algorithm consists of a Gabor filter that detects the switching pattern and employs the binarization method to extract the shape of the defect. The optics module and detection algorithm optimized using a simulator were installed at a real plant, and the experimental results conducted on thick steel plate images obtained from the steel production line show the effectiveness of the proposed method.

Magnetic Sensor for Building Structural Vibrations

PubMed Central

García, Alfonso; Morón, Carlos; Tremps, Enrique

2014-01-01

This paper shows a new displacement-to-frequency transducer based on the variation of a coil inductance when a magnetic core is partially or completely inserted inside. This transducer is based on a Colpitts oscillator due its low manufacturing price, behavior and immunity to noise. A tank circuit with a configuration in parallel was used because it can be employed at lower frequencies and it enables it to make a direct analysis. The sensor has a dynamic range equal to the length of the coil. The cores can exchange sensors (coils with its ferromagnetic core) using the same electronic measuring system. In this way, with only an electronic circuit, the core sensor determines the measurement range. The obtained resolution is higher than 1/100,000, and the sensor also allows the measurement and knowing in real time the effect of vibration, thermal expansion, referred overload movements, etc.., that can occur in the structural elements of a building. PMID:24504104

Assessment of possible failure modes and non-destructive examination of the ITER pre-compression rings

NASA Astrophysics Data System (ADS)

Knaster, J.; Evans, D.; Rajainmaki, H.

2012-06-01

The pre-compression rings (PCRs) for the International Thermonuclear Experimental Reactor (ITER) represent one of the largest and most highly stressed composite structures ever designed for long term operation at 4K. Three rings, each 5m in diameter and 337 × 288 mm in cross-section, will be installed at the top and bottom of the eighteen "D" shaped Toroidal Field (TF) coils to apply a total centripetal load of 70 MN per TF coil. The interaction of the 68 kA conductor current circulating in the coil (for a total of 9.1MA) with the required magnetic field to confine the plasma during operation will result in Lorentz forces that build in-plane and out-of-plane loads. The PCRs are essential to keep the stresses below the acceptable level for the ITER magnets structural materials.

Coiled-coil length: Size does matter.

PubMed

Surkont, Jaroslaw; Diekmann, Yoan; Ryder, Pearl V; Pereira-Leal, Jose B

2015-12-01

Protein evolution is governed by processes that alter primary sequence but also the length of proteins. Protein length may change in different ways, but insertions, deletions and duplications are the most common. An optimal protein size is a trade-off between sequence extension, which may change protein stability or lead to acquisition of a new function, and shrinkage that decreases metabolic cost of protein synthesis. Despite the general tendency for length conservation across orthologous proteins, the propensity to accept insertions and deletions is heterogeneous along the sequence. For example, protein regions rich in repetitive peptide motifs are well known to extensively vary their length across species. Here, we analyze length conservation of coiled-coils, domains formed by an ubiquitous, repetitive peptide motif present in all domains of life, that frequently plays a structural role in the cell. We observed that, despite the repetitive nature, the length of coiled-coil domains is generally highly conserved throughout the tree of life, even when the remaining parts of the protein change, including globular domains. Length conservation is independent of primary amino acid sequence variation, and represents a conservation of domain physical size. This suggests that the conservation of domain size is due to functional constraints. © 2015 Wiley Periodicals, Inc.

Fabrication of First 4-m Coils for the LARP MQXFA Quadrupole and Assembly in Mirror Structure

DOE PAGES

Holik, Eddie Frank; Ambrosio, Giorgio; Anerella, Michael; ...

2017-01-23

The US LHC Accelerator Research Program is constructing prototype interaction region quadrupoles as part of the US in-kind contribution to the Hi-Lumi LHC project. The low-beta MQXFA Q1/Q3 coils have a 4-m length and a 150 mm bore. The design is first validated on short, one meter models (MQXFS) developed as part of the longstanding Nb3Sn quadrupole R&D by LARP in collaboration with CERN. In parallel, facilities and tooling are being developed and refined at BNL, LBNL, and FNAL to enable long coil production, assembly, and cold testing. Long length scale-up is based on the experience from the LARP 90more » mm aperture (TQ-LQ) and 120 mm aperture (HQ and Long HQ) programs. A 4-m long MQXF practice coil was fabricated, water jet cut and analyzed to verify procedures, parts, and tooling. In parallel, the first complete prototype coil (QXFP01a) was fabricated and assembled in a long magnetic mirror, MQXFPM1, to provide early feedback on coil design and fabrication following the successful experience of previous LARP mirror tests.« less

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

NASA Astrophysics Data System (ADS)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

NMR Model of PrgI-SipD Interaction and its Implications in the Needle-Tip Assembly of the Salmonella Type III Secretion System

PubMed Central

Rathinavelan, Thenmalarchelvi; Lara-Tejero, Maria; Lefebre, Matthew; Chatterjee, Srirupa; McShan, Andrew C.; Guo, Da-Chuan; Tang, Chun; Galan, Jorge E.; De Guzman, Roberto N.

2014-01-01

Salmonella and other pathogenic bacteria use the type III secretion system (T3SS) to inject virulence proteins into human cells to initiate infections. The structural component of the T3SS contains a needle and a needle tip. The needle is assembled from PrgI needle protomers and the needle tip is capped with several copies of the SipD tip protein. How a tip protein docks on the needle is unclear. A crystal structure of a PrgI-SipD fusion protein docked on the PrgI needle results in steric clash of SipD at the needle tip when modeled on the recent atomic structure of the needle. Thus, there is currently no good model of how SipD is docked on the PrgI needle tip. Previously, we showed by NMR paramagnetic relaxation enhancement (PRE) methods that a specific region in the SipD coiled-coil is the binding site for PrgI. Others have hypothesized that a domain of the tip protein – the N-terminal α-helical hairpin, has to swing away during the assembly of the needle apparatus. Here, we show by PRE methods that a truncated form of SipD lacking the α-helical hairpin domain binds more tightly to PrgI. Further, PRE-based structure calculations revealed multiple PrgI binding sites on the SipD coiled-coil. Our PRE results together with the recent NMR-derived atomic structure of the Salmonella needle suggest a possible model of how SipD might dock at the PrgI needle tip. SipD and PrgI are conserved in other bacterial T3SSs, thus our results have wider implication in understanding other needle-tip complexes. PMID:24951833

Crystallographic Studies of Intermediate Filament Proteins.

PubMed

Guzenko, Dmytro; Chernyatina, Anastasia A; Strelkov, Sergei V

Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical 'rod' domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the 'signature feature' of the IF family. Bioinformatics analysis reveals that the rod domain of all IF proteins contains three α-helical segments of largely conserved length, interconnected by linkers. Moreover, there is a conserved pattern of hydrophobic repeats within each segment, which includes heptads and hendecads. This defines the presence of both left-handed and almost parallel coiled-coil regions along the rod length. Using X-ray crystallography on multiple overlapping fragments of IF proteins, the atomic structure of the nearly complete rod domain has been determined. Here, we discuss some specific challenges of this procedure, such as crystallization and diffraction data phasing by molecular replacement. Further insights into the structure of the coiled coil and the terminal domains have been obtained using electron paramagnetic resonance measurements on the full-length protein, with spin labels attached at specific positions. This atomic resolution information, as well as further interesting findings, such as the variation of the coiled-coil stability along the rod length, provide clues towards interpreting the data on IF assembly, collected by a range of methods. However, a full description of this process at the molecular level is not yet at hand.

Optimized 14 + 1 receive coil array and position system for 3D high-resolution MRI of dental and maxillomandibular structures.

PubMed

Sedlacik, Jan; Kutzner, Daniel; Khokale, Arun; Schulze, Dirk; Fiehler, Jens; Celik, Turgay; Gareis, Daniel; Smeets, Ralf; Friedrich, Reinhard E; Heiland, Max; Assaf, Alexandre T

2016-01-01

The purpose of this study was to design, build and test a multielement receive coil array and position system, which is optimized for three-dimensional (3D) high-resolution dental and maxillomandibular MRI with high patient comfort. A 14 + 1 coil array and positioning system, allowing easy handling by the technologists, reproducible positioning of the patients and high patient comfort, was tested with three healthy volunteers using a 3.0-T MRI machine (Siemens Skyra; Siemens Medical Solutions, Erlangen, Germany). High-resolution 3D T1 weighted, water excitation T1 weighted and fat-saturated T2 weighted imaging sequences were scanned, and 3D image data were reformatted in different orientations and curvatures to aid diagnosis. The high number of receiving coils and the comfortable positioning of the coil array close to the patient's face provided a high signal-to-noise ratio and allowed high quality, high resolution, 3D image data to be acquired within reasonable scan times owing to the possibility of parallel image acquisition acceleration. Reformatting the isotropic 3D image data in different views is helpful for diagnosis, e.g. panoramic reconstruction. The visibility of soft tissues such as the mandibular canal, nutritive canals and periodontal ligaments was exquisite. The optimized MRI receive coil array and positioning system for dental and oral-maxillofacial imaging provides a valuable tool for detecting and diagnosing pathologies in dental and oral-maxillofacial structures while avoiding radiation dose. The high patient comfort, as achieved by our design, is very crucial, since image artefacts due to movement or failing to complete the examination jeopardize the diagnostic value of MRI examinations.

Eddy current simulation in thick cylinders of finite length induced by coils of arbitrary geometry.

PubMed

Sanchez Lopez, Hector; Poole, Michael; Crozier, Stuart

2010-12-01

Eddy currents are inevitably induced when time-varying magnetic field gradients interact with the metallic structures of a magnetic resonance imaging (MRI) scanner. The secondary magnetic field produced by this induced current degrades the spatial and temporal performance of the primary field generated by the gradient coils. Although this undesired effect can be minimized by using actively and/or passively shielded gradient coils and current pre-emphasis techniques, a residual eddy current still remains in the MRI scanner structure. Accurate simulation of these eddy currents is important in the successful design of gradient coils and magnet cryostat vessels. Efficient methods for simulating eddy currents are currently restricted to cylindrical-symmetry. The approach presented in this paper divides thick conducting cylinders into thin layers (thinner than the skin depth) and expresses the current density on each as a Fourier series. The coupling between each mode of the Fourier series with every other is modeled with an inductive network method. In this way, the eddy currents induced in realistic cryostat surfaces by coils of arbitrary geometry can be simulated. The new method was validated by simulating a canonical problem and comparing the results against a commercially available software package. An accurate skin depth of 2.76 mm was calculated in 6 min with the new method. The currents induced by an actively shielded x-gradient coil were simulated assuming a finite length cylindrical cryostat consisting of three different conducting materials. Details of the temporal-spatial induced current diffusion process were simulated through all cryostat layers, which could not be efficiently simulated with any other method. With this data, all quantities that depend on the current density, such as the secondary magnetic field, are simply evaluated. Copyright © 2010 Elsevier Inc. All rights reserved.

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.

PubMed

Koliopoulos, Marios G; Esposito, Diego; Christodoulou, Evangelos; Taylor, Ian A; Rittinger, Katrin

2016-06-01

TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin-loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full-length protein. Our data reveal an unexpected diversity in the self-association mechanism of TRIMs that might be crucial for their biological function. © 2016 Francis Crick Institute. Published under the terms of the CC BY 4.0 license.

The fatigue evaluation method for a structural stainless steel using the magnetic sensor composed of three pancake coils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oka, M.; Tsuchida, Y.; Enokizono, M.

May metallic structural materials, such as stainless steels, are currently used in our surroundings. If external force is repeatedly added for many years, it is thought that fatigue damage accumulates in stainless steels. When excessive fatigue damage accumulates in these metals, there is a possibility that they are destroyed by fatigue damage accumulation. Therefore, it is important to know the amount of the fatigue damage they have suffered in order to prevent them from being destroyed. We are developing the fatigue evaluation method for stainless steels with a magnetic sensor composed of three pancake type coils. In this research, themore » inspection object is ferritic stainless steels such as SUS430. The method of fatigue evaluation for ferritic stainless steels uses the three coil type sensor, and shows a good correlation between the number of stress cycles and the output signal of the sensor, even though the correlation between the output signal and an added stress is not completely accurate. This paper describes the evaluation method of fatigue damage in ferritic stainless steel using a magnetic sensor composed of three pancake-type coils.« less

Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif

PubMed Central

Wang, Yaofeng; Kraut, Rachel; Mu, Yuguang

2015-01-01

The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ. PMID:26540054

Membrane fusion activity of vesicular stomatitis virus glycoprotein G is induced by low pH but not by heat or denaturant.

PubMed

Yao, Yi; Ghosh, Kakoli; Epand, Raquel F; Epand, Richard M; Ghosh, Hara P

2003-06-05

The fusogenic envelope glycoprotein G of the rhabdovirus vesicular stomatitis virus (VSV) induces membrane fusion at acidic pH. At acidic pH the G protein undergoes a major structural reorganization leading to the fusogenic conformation. However, unlike other viral fusion proteins, the low-pH-induced conformational change of VSV G is completely reversible. As well, the presence of an alpha-helical coiled-coil motif required for fusion by a number of viral and cellular fusion proteins was not predicted in VSV G protein by using a number of algorithms. Results of pH dependence of the thermal stability of G protein as determined by intrinsic Trp fluorescence and circular dichroism (CD) spectroscopy show that the G protein is equally stable at neutral or acidic pH. Destabilization of G structure at neutral pH with either heat or urea did not induce membrane fusion or conformational change(s) leading to membrane fusion. Taken together, these data suggest that the mechanism of VSV G-induced fusion is distinct from the fusion mechanism of fusion proteins that involve a coiled-coil motif.

Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor.

PubMed

Abriata, Luciano A; Albanesi, Daniela; Dal Peraro, Matteo; de Mendoza, Diego

2017-06-20

Histidine kinases (HK) are the sensory proteins of two-component systems, responsible for a large fraction of bacterial responses to stimuli and environmental changes. Prototypical HKs are membrane-bound proteins that phosphorylate cognate response regulator proteins in the cytoplasm upon signal detection in the membrane or periplasm. HKs stand as potential drug targets but also constitute fascinating systems for studying proteins at work, specifically regarding the chemistry and mechanics of signal detection, transduction through the membrane, and regulation of catalytic outputs. In this Account, we focus on Bacillus subtilis DesK, a membrane-bound HK part of a two-component system that maintains appropriate membrane fluidity at low growth temperatures. Unlike most HKs, DesK has no extracytoplasmic signal-sensing domains; instead, sensing is carried out by 10 transmembrane helices (coming from two protomers) arranged in an unknown structure. The fifth transmembrane helix from each protomer connects, without any of the intermediate domains found in other HKs, into the dimerization and histidine phosphotransfer (DHp) domain located in the cytoplasm, which is followed by the ATP-binding domains (ABD). Throughout the years, genetic, biochemical, structural, and computational studies on wild-type, mutant, and truncated versions of DesK allowed us to dissect several aspects of DesK's functioning, pushing forward a more general understanding of its own structure/function relationships as well as those of other HKs. We have shown that the sensing mechanism is rooted in temperature-dependent membrane properties, most likely a combination of thickness, fluidity, and water permeability, and we have proposed possible mechanisms by which DesK senses these properties and transduces the signals. X-ray structures and computational models have revealed structural features of TM and cytoplasmic regions in DesK's kinase- and phosphatase-competent states. Biochemical and genetic experiments and molecular simulations further showed that reversible formation of a two-helix coiled coil in the fifth TM segment and the N-terminus of the cytoplasmic domain is essential for the sensing and signal transduction mechanisms. Together with other structural and functional works, the emerging picture suggests that diverse HKs possess distinct sensing and transduction mechanisms but share as rather general features (i) a symmetric phosphatase state and an asymmetric kinase state and (ii) similar functional outputs on the conserved DHp and ABD domains, achieved through different mechanisms that depend on the nature of the initial signal. We here advance (iii) an important role for TM prolines in transducing the initial signals to the cytoplasmic coiled coils, based on simulations of DesK's TM helices and our previous work on a related HK, PhoQ. Lastly, evidence for DesK, PhoQ, BvgS, and DctB HKs shows that (iv) overall catalytic output is tuned by a delicate balance between hydration potentials, coiled coil stability, and exposure of hydrophobic surface patches at their cytoplasmic coiled coils and at the N-terminal and C-terminal sides of their TM helices. This balance is so delicate that small perturbations, either physiological signals or induced by mutations, lead to large remodeling of the underlying conformational landscape achieving clear-cut changes in catalytic output, mirroring the required response speed of these systems for proper biological function.

Design and fabrication of a superconducting magnet for an 18 GHz electron cyclotron resonance ion∕photon source NFRI-ECRIPS.

PubMed

You, H-J; Jang, S-W; Jung, Y-H; Lho, T-H; Lee, S-J

2012-02-01

A superconducting magnet was designed and fabricated for an 18 GHz ECR ion∕photon source, which will be installed at National Fusion Research Institute (NFRI) in South Korea. The magnetic system consists of a set of four superconducting coils for axial mirror field and 36 pieces of permanent magnets for hexapolar field. The superconducting coils with a cryocooler (1.5 W @ 4.2 K) allow one to reach peak mirror fields of 2.2 T in the injection and those of 1.5 T in the extraction regions on the source axis, and the resultant hexapolar field gives 1.35 T on the plasma chamber wall. The unbalanced magnetic force between the coils and surrounding yoke has been minimized to 16 ton by a coil arrangement and their electrical connection, and then was successfully suspended by 12 strong thermal insulating supports made of large numbers of carbon fibers. In order to block radiative thermal losses, multilayer thermal insulations are covered on the coil windings as well as 40-K aluminum thermal shield. Also new schemes of quench detection and safety system (coil divisions, quench detection coils, and heaters) were employed. For impregnation of the windings a special epoxy has been selected and treated to have a higher breaking strength and a higher thermal conductivity, which enables the superconductors to be uniformly and rapidly cooled down or heated during a quench.

Vibration and shape control of hinged light structures using electromagnetic forces

NASA Astrophysics Data System (ADS)

Matsuzaki, Yuji; Miyachi, Shigenobu; Sasaki, Toshiyuki

2003-08-01

This paper describes a new electromagnetic device for vibration control of a light-weighted deployable/retractable structure which consists of many small units connected with mechanical hinges. A typical example of such a structure is a solar cell paddle of an artificial satellite which is composed of many thin flexible blankets connected in series. Vibration and shape control of the paddle is not easy, because control force and energy do not transmit well between the blankets which are discretely connected by hinges with each other. The new device consists of a permanent magnet glued along an edge of a blanket and an electric current-conducting coil glued along an adjoining edge of another adjacent blanket. Conduction of the electric current in a magnetic field from the magnet generates an electromagnetic force on the coil. By changing the current in the coil, therefore, we may control the vibration and shape of the blankets. To confirm the effectiveness of the new device, constructing a simple paddle model consisting eight hinge- panels, we have carried out a model experiment of vibration and shape control of the paddle. In addition, a numerical simulation of vibration control of the hinge structure is performed to compare with measured data.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.

PubMed

Bruhn, Jessica F; Kirchdoerfer, Robert N; Urata, Sarah M; Li, Sheng; Tickle, Ian J; Bricogne, Gérard; Saphire, Erica Ollmann

2017-01-15

Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (genera Marburgvirus and Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. Marburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics. Copyright © 2017 American Society for Microbiology.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.

ABSTRACT Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOVmore » VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics.« less

TEM Systems Design: Using Full Maxwell FDTD Modelling to Study the Transient Response of Custom-madeTx and Rx Coils.

NASA Astrophysics Data System (ADS)

Chevalier, A.; Rejiba, F.; Schamper, C.; Thiesson, J.; Hovhannissian, G.

2016-12-01

From airborne applications to field scale measurements of Transient Electromagnetic Methods(TEM), an accurate knowledge of the sensitivity of the inductive coil sensors (system response) is aprerequisite to interpret the measured transient magnetic flux density into a subsurface distributionof conductivity. The system response is a term that refers to the cumulative effect of inductive andcapacitive couplings (cross-talks) between each component constituting a TEM apparatus and thenearby conductive structures. As a result, the frequency sensitivity of the voltage coil sensor (Rx)along with the emitted current waveform in the current emitting coil (Tx) are controlled by thegeometry and electronic characteristic of the set-up as well as the near surface electromagneticproperties. During the early development of an innovative airborne TEM solutions (French nationalTEMas project), determining the coil geometries and the impedance matching between all parts ofthe transmission link (electronic parts and coils) for various environmental set-ups, has been a majorissue. In this study, we review the required theoretical framework and propose a versatile numericalmethodology to ease the coil design and impedance matching process while extending ourunderstanding of short-time transient that operates from DC to moderately high frequencies (0 to 20Mhz). We used a full Maxwell equations FDTD model along with a semi-analytical 1D modeler to infercoils emitting and receiving properties, for various coil geometries and site-dependent conditions.Results highlight the influence of the environment on the emitting and sensing properties. Theincreasing effects of cross-talks between the Tx and the Rx coils depending on their size is shown.Strategies regarding the impedance adaptation between the electronical components and the coilsensors are then discussed for different geophysical specifications.

An Update on Structural Seal Development at NASA GRC

NASA Technical Reports Server (NTRS)

Dunlap, Pat; Steinetz, Bruce; Finkbeiner, Josh; DeMange, Jeff; Taylor, Shawn; Daniels, Chris; Oswald, Jay

2006-01-01

A viewgraph presentation describing advanced structural seal development for NASA exploration is shown. The topics include: 1) GRC Structural Seals Team Research Areas; 2) Research Areas & Objective; 3) Wafer Seal Geometry/Flow Investigations; 4) Wafer Seal Installation DOE Study; 5) Results of Wafer Seal Installation DOE Study; 6) Wafer Geometry Study: Thickness Variations; 7) Wafer Geometry Study: Full-Size vs. Half-Size Wafers; 8) Spring Tube Seal Development; 9) Resiliency Improvement for Rene 41 Spring Tube; 10) Spring Tube Seals: Go-Forward Plan; 11) High Temperature Seal Preloader Development: TZM Canted Coil Spring; 12) TZM Canted Coil Spring Development; 13) Arc Jet Test Rig Development; and 14) Arc Jet Test Rig Status.

Influences on water-hammer wave shape: an experimental study

NASA Astrophysics Data System (ADS)

Traudt, T.; Bombardieri, C.; Manfletti, C.

2016-09-01

Water-hammer phenomena are of strong interest in a number of different industrial fields, amongst which the space industry. Here the priming of feedlines during start-up of an engine as well as the rapid closing of valves upon shutdown may lead to pressure peaks symptomatic of a water-hammer wave. Test benches used to conduct tests on future as well as current engines are also sensitive to water-hammer waves traveling along their feedlines. To enhance the understanding of water-hammer, we investigated different configurations and their influence on the wave shape in the frequency domain. The configurations feature a coiled pipe setup with a support structure and without a support structure. Two other phenomena will be presented. We found a beat phenomenon which is likely to be the so called Poisson-coupling beat. Finally we will show that the second water-hammer peak can reach pressures a lot higher than the first peak by additive interference of the primary and secondary water-hammer wave.

Fault current limiter

DOEpatents

Darmann, Francis Anthony

2013-10-08

A fault current limiter (FCL) includes a series of high permeability posts for collectively define a core for the FCL. A DC coil, for the purposes of saturating a portion of the high permeability posts, surrounds the complete structure outside of an enclosure in the form of a vessel. The vessel contains a dielectric insulation medium. AC coils, for transporting AC current, are wound on insulating formers and electrically interconnected to each other in a manner such that the senses of the magnetic field produced by each AC coil in the corresponding high permeability core are opposing. There are insulation barriers between phases to improve dielectric withstand properties of the dielectric medium.

Identification of a "glycine-loop"-like coiled structure in the 34 AA Pro,Gly,Met repeat domain of the biomineral-associated protein, PM27.

PubMed

Wustman, Brandon A; Santos, Rudolpho; Zhang, Bo; Evans, John Spencer

2002-12-05

Fracture resistance in biomineralized structures has been linked to the presence of proteins, some of which possess sequences that are associated with elastic behavior. One such protein superfamily, the Pro,Gly-rich sea urchin intracrystalline spicule matrix proteins, form protein-protein supramolecular assemblies that modify the microstructure and fracture-resistant properties of the calcium carbonate mineral phase within embryonic sea urchin spicules and adult sea urchin spines. In this report, we detail the identification of a repetitive keratin-like "glycine-loop"- or coil-like structure within the 34-AA (AA: amino acid) N-terminal domain, (PGMG)(8)PG, of the spicule matrix protein, PM27. The identification of this repetitive structural motif was accomplished using two capped model peptides: a 9-AA sequence, GPGMGPGMG, and a 34-AA peptide representing the entire motif. Using CD, NMR spectrometry, and molecular dynamics simulated annealing/minimization simulations, we have determined that the 9-AA model peptide adopts a loop-like structure at pH 7.4. The structure of the 34-AA polypeptide resembles a coil structure consisting of repeating loop motifs that do not exhibit long-range ordering. Given that loop structures have been associated with protein elastic behavior and protein motion, it is plausible that the 34-AA Pro,Gly,Met repeat sequence motif in PM27 represents a putative elastic or mobile domain. Copyright 2002 Wiley Periodicals, Inc.

Application of statistical methods to reveal and remove the causes of welding of coil laps upon annealing of cold-rolled steel strips

NASA Astrophysics Data System (ADS)

Garber, E. A.; Diligenskii, E. V.; Antonov, P. V.; Shalaevskii, D. L.; Dyatlov, I. A.

2017-09-01

The factors of the process of production of cold-rolled steel strips that promote and hinder the appearance of a coil lap welding defect upon annealing in bell-type furnaces are analyzed using statistical methods. The works dealing with this problem are analytically reviewed to reveal the problems to be studied and refined. The ranking of the technological factors according to the significance of their influence on the probability of appearance of this defect is determined and supported by industrial data, and a regression equation is derived to calculate this probability. The process of production is improved to minimize the rejection of strips caused by the welding of coil laps.

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure.

PubMed

Chiusano, M L; D'Onofrio, G; Alvarez-Valin, F; Jabbari, K; Colonna, G; Bernardi, G

1999-09-30

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (alpha-helix, beta-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be alpha-helix, beta-sheet, or coil. Likewise, the nonsynonymous rates also differ, although expectedly at a lower extent, in the three types of secondary structure, suggesting that different selective constraints associated with the different structures are affecting in a similar way the synonymous and nonsynonymous rates. Moreover, the base composition of the third codon positions is different in coding sequence regions corresponding to different secondary structures of proteins.

Low Frequency Radio-wave System for subsurface investigation

NASA Astrophysics Data System (ADS)

Soldovieri, Francesco; Gennarelli, Gianluca; Kudelya, Anatoliy; Denisov, Alexander

2015-04-01

Low frequency radio-wave methods (RWM) allow subsurface investigations in terms of lithological structure characterization, detection of filtration flows of ground water, anthropogenic and natural cavities. In this contribution, we present a RWM that exploits two coils working at frequencies of few MHz as transmitting and receiving antennas. The basic principle of this inductive method is as follows. The primary alternating electromagnetic field radiated by the transmitting coil induces eddy currents in the subsurface mainly due to the conductivity anomalies. These eddy currents generate a secondary (scattered) magnetic field which overlaps to the incident magnetic field and is detected by the receiving coil. Despite the simple operation of the system, the complexity of the electromagnetic scattering phenomenon at hand must be properly modeled to achieve adequate performance. Therefore, an advanced data processing technique, belonging to the class of the inverse scattering approaches, has been developed by the authors in a full 3D geometry. The proposed method allows to deal with data collected on a scanning surface under a dipole inductive profiling (DIP) modality, where the transmitting/receiving coils are moved simultaneously with fixed offset (multi-bistatic configuration). The hardware, called Dipole Inductive Radio-wave System (DIRS), is composed by an electronic unit and transmitting and receiving loop antennas radiating at frequencies of few MHz (2-4 MHz), which are installed on theodolite supports. The compactness of DIRS and its robustness to external electromagnetic interference offers the possibility to perform geophysical research up to the depth of some tens of meters and under several types of ground and water surfaces, vegetation, and weather conditions. The light weight and small size of system (the single antenna with support weights about 5 kg and has a diameter of 0.5m) allows two operators to perform geophysical research without disturbing the surface integrity of investigated ground massif. The value of base and the value of voltage induced on the digital voltmeter of the receiver are stored in memory on a SD-card for a subsequent visualization and processing. Realistic cases of application of the DIRS system enhanced by the inverse scattering approach will be presented at the conference with regard to the geological characterization of a mine shaft and an archaeological site.

Structural characteristics and properties of the regenerated silk fibroin prepared from formic acid.

PubMed

Um, I C; Kweon, H Y; Park, Y H; Hudson, S

2001-08-20

Structural characteristics and thermal and solution properties of the regenerated silk fibroin (SF) prepared from formic acid (FU) were compared with those of SF from water (AU). According to the turbidity and shear viscosity measurement, SF formic acid solution was stable and transparent, no molecular aggregations occurred. The sample FU exhibited the beta-sheet structure, while AU random coil conformation using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and differential scanning calorimetry. The effects of methanol treatment on samples were also examined. According to the measurement of crystallinity (XRD) and crystallinity index (FTIR), the concept of long/short-range ordered structure formation was proposed. Long-range ordered crystallites are predominantly formed for methanol treated SF film while SF film cast from formic acid favors the formation of short-range ordered structure. The relaxation temperatures of SF films measured by dynamic thermomechanical analysis supported the above mechanism due to the sensitivity of relaxation temperature on the short-range order.

An efficient calibration method for SQUID measurement system using three orthogonal Helmholtz coils

NASA Astrophysics Data System (ADS)

Hua, Li; Shu-Lin, Zhang; Chao-Xiang, Zhang; Xiang-Yan, Kong; Xiao-Ming, Xie

2016-06-01

For a practical superconducting quantum interference device (SQUID) based measurement system, the Tesla/volt coefficient must be accurately calibrated. In this paper, we propose a highly efficient method of calibrating a SQUID magnetometer system using three orthogonal Helmholtz coils. The Tesla/volt coefficient is regarded as the magnitude of a vector pointing to the normal direction of the pickup coil. By applying magnetic fields through a three-dimensional Helmholtz coil, the Tesla/volt coefficient can be directly calculated from magnetometer responses to the three orthogonally applied magnetic fields. Calibration with alternating current (AC) field is normally used for better signal-to-noise ratio in noisy urban environments and the results are compared with the direct current (DC) calibration to avoid possible effects due to eddy current. In our experiment, a calibration relative error of about 6.89 × 10-4 is obtained, and the error is mainly caused by the non-orthogonality of three axes of the Helmholtz coils. The method does not need precise alignment of the magnetometer inside the Helmholtz coil. It can be used for the multichannel magnetometer system calibration effectively and accurately. Project supported by the “Strategic Priority Research Program (B)” of the Chinese Academy of Sciences (Grant No. XDB04020200) and the Shanghai Municipal Science and Technology Commission Project, China (Grant No. 15DZ1940902).

Effects of coil orientation on the electric field induced by TMS over the hand motor area

NASA Astrophysics Data System (ADS)

Laakso, Ilkka; Hirata, Akimasa; Ugawa, Yoshikazu

2014-01-01

Responses elicited by transcranial magnetic stimulation (TMS) over the hand motor area depend on the position and orientation of the stimulating coil. In this work, we computationally investigate the induced electric field for multiple coil orientations and locations in order to determine which parts of the brain are affected and how the sensitivity of motor cortical activation depends on the direction of the electric field. The finite element method is used for calculating the electric field induced by TMS in two individual anatomical models of the head and brain. The orientation of the coil affects both the strength and depth of penetration of the electric field, and the field strongly depends on the direction of the sulcus, where the target neurons are located. The coil position that gives the strongest electric field in the target cortical region may deviate from the closest scalp location by a distance on the order of 1 cm. Together with previous experimental data, the results support the hypothesis that the cortex is most sensitive to fields oriented perpendicular to the cortical layers, while it is relatively insensitive to fields parallel to them. This has important implications for targeting of TMS. To determine the most effective coil position and orientation, it is essential to consider both biological (the direction of the targeted axons) and physical factors (the strength and direction of the electric field).

Langmuir Probe Measurements in an Inductively Coupled GEC Reference Cell Plasma

NASA Technical Reports Server (NTRS)

Ji, J. S.; Kim, J. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, J. O. (Technical Monitor)

1998-01-01

Measurements of electron number density, electron temperature, and electron energy distribution function (EEDF) using a compensated Langmuir probe have been performed on an inductively (transformer ) coupled Gaseous Electronics Conference (GEC) reference cell plasma. The plasma source is operated with CH4, CF4, or their mixtures with argon. The effect of independently driving the electrode supporting the wafer on the probe data is studied. In particular, we find that the plasma structure depends on the phase in addition to the magnitude of the power coupled to the electrode relative to that of the transformer coil. The Langmuir probe is translated in a plane parallel to the electrode to investigate the spatial structure of the plasma. The probe data is also compared with fluid model predictions.

Design of a dee vacuum vessel for Doublet III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, L.G.

1983-04-01

The Doublet III tokamak is to be modified wherein the original 'doublet' plasma containment vacuum vessel will be exchanged with one of a large dee-shaped cross section. The basic dimensions of the dee vessel will allow plasmas of 1.7-m major radius, 0.7-m minor radius, and a vertical elongation of 1.8. Installation of a large dee vessel in Doublet III is made possible by the demountable toroidal field coils and the large, low-ripple volume they include. Ripple at the plasma edge will be less than one percent. The plasma parameters affecting the design of the vessel will be reviewed including plasmamore » current, power, disruption time, allowable error field, impurity control techniques, pulse length, and limiter schemes. A driving requirement for the design of the vessel is to maximize the access to the plasma for auxiliary heating (both neutral beam injection and radio frequency heating), diagnostics, developmental component and material testing, and pumping. The dee vessel is structurally designed along the same lines as the present vessel: an Inconel 625, all-welded, continuous chamber in a corrugated sandwich construction. An overview of the vessel design and its solutions to the design criteria will be presented. An overview will also be presented of the entire modification project which includes replacement of some coils, and addition of support structure, limiters and vessel armor, and power system components.« less

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin

NASA Astrophysics Data System (ADS)

Verly, Rodrigo M.; Resende, Jarbas M.; Junior, Eduardo F. C.; de Magalhães, Mariana T. Q.; Guimarães, Carlos F. C. R.; Munhoz, Victor H. O.; Bemquerer, Marcelo Porto; Almeida, Fábio C. L.; Santoro, Marcelo M.; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-01

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays.

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin

PubMed Central

Verly, Rodrigo M.; Resende, Jarbas M.; Junior, Eduardo F. C.; de Magalhães, Mariana T. Q.; Guimarães, Carlos F. C. R.; Munhoz, Victor H. O.; Bemquerer, Marcelo Porto; Almeida, Fábio C. L.; Santoro, Marcelo M.; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-01

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays. PMID:28102305

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin.

PubMed

Verly, Rodrigo M; Resende, Jarbas M; Junior, Eduardo F C; de Magalhães, Mariana T Q; Guimarães, Carlos F C R; Munhoz, Victor H O; Bemquerer, Marcelo Porto; Almeida, Fábio C L; Santoro, Marcelo M; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-19

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays.

On the glitches in the force transmitted by an electrodynamic exciter to a structure

NASA Technical Reports Server (NTRS)

Rao, Dantam K.

1987-01-01

Around resonance, the force transmitted by an exciter into a structure will be smaller or greater than a reference force generated by its coils due to electromechanical interaction. A simple analysis is presented which reveals how this phenomenon of force drop-off is controlled by three factors. The first factor, called Armature Mass Factor, describes a purely mechanical interaction between the structure and the exciter. The electromechanical energy conversion and its interaction with the structure yields two additional factors, called Electrical Resistance and Electrical Inductance Factors. They describe the effects of coil resistance, inductance and magnetic field strength relative to structural damping and stiffness. Present analysis indicates that, under proper circumstances, more than 90 percent of the force drop-off can be eliminated if armature-to-structure mass ratio is smaller or equal to half of modal loss factor.

A Novel Transient Fault Current Sensor Based on the PCB Rogowski Coil for Overhead Transmission Lines

PubMed Central

Liu, Yadong; Xie, Xiaolei; Hu, Yue; Qian, Yong; Sheng, Gehao; Jiang, Xiuchen

2016-01-01

The accurate detection of high-frequency transient fault currents in overhead transmission lines is the basis of malfunction detection and diagnosis. This paper proposes a novel differential winding printed circuit board (PCB) Rogowski coil for the detection of transient fault currents in overhead transmission lines. The interference mechanism of the sensor surrounding the overhead transmission line is analyzed and the guideline for the interference elimination is obtained, and then a differential winding printed circuit board (PCB) Rogowski coil is proposed, where the branch and return line of the PCB coil were designed to be strictly symmetrical by using a joining structure of two semi-rings and collinear twisted pair differential windings in each semi-ring. A serial test is conducted, including the frequency response, linearity, and anti-interference performance as well as a comparison with commercial sensors. Results show that a PCB Rogowski coil has good linearity and resistance to various external magnetic field interferences, thus enabling it to be widely applied in fault-current-collecting devices. PMID:27213402

Stress and Thermal Analysis of the In-Vessel Resonant Magnetic Perturbation Coils on the J-TEXT Tokamak

NASA Astrophysics Data System (ADS)

Hao, Changduan; Zhang, Ming; Ding, Yonghua; Rao, Bo; Cen, Yishun; Zhuang, Ge

2012-01-01

A set of four in-vessel saddle coils was designed to generate a helical field on the J-TEXT tokamak to study the influences of the external perturbation field on plasma. The coils are fed with alternating current up to 10 kA at frequency up to 10 kHz. Due to the special structure, complex thermal environment and limited space in the vacuum chamber, it is very important to make sure that the coils will not be damaged when undergoing the huge electromagnetic forces in the strong toroidal field, and that their temperatures don't rise too much and destroy the insulation. A 3D finite element model is developed in this paper using the ANSYS code, stresses are analyzed to find the worst condition, and a mounting method is then established. The results of the stress and modal analyses show that the mounting method meets the strength requirements. Finally, a thermal analysis is performed to study the cooling process and the temperature distribution of the coils.

Finite element coiled cochlea model

NASA Astrophysics Data System (ADS)

Isailovic, Velibor; Nikolic, Milica; Milosevic, Zarko; Saveljic, Igor; Nikolic, Dalibor; Radovic, Milos; Filipović, Nenad

2015-12-01

Cochlea is important part of the hearing system, and thanks to special structure converts external sound waves into neural impulses which go to the brain. Shape of the cochlea is like snail, so geometry of the cochlea model is complex. The simplified cochlea coiled model was developed using finite element method inside SIFEM FP7 project. Software application is created on the way that user can prescribe set of the parameters for spiral cochlea, as well as material properties and boundary conditions to the model. Several mathematical models were tested. The acoustic wave equation for describing fluid in the cochlea chambers - scala vestibuli and scala timpani, and Newtonian dynamics for describing vibrations of the basilar membrane are used. The mechanical behavior of the coiled cochlea was analyzed and the third chamber, scala media, was not modeled because it does not have a significant impact on the mechanical vibrations of the basilar membrane. The obtained results are in good agreement with experimental measurements. Future work is needed for more realistic geometry model. Coiled model of the cochlea was created and results are compared with initial simplified coiled model of the cochlea.

Feasibility Study on Active Back Telemetry and Power Transmission Through an Inductive Link for Millimeter-Sized Biomedical Implants.

PubMed

Yeon, Pyungwoo; Mirbozorgi, S Abdollah; Lim, Jaemyung; Ghovanloo, Maysam

2017-12-01

This paper presents a feasibility study of wireless power and data transmission through an inductive link to a 1-mm 2 implant, to be used as a free-floating neural probe, distributed across a brain area of interest. The proposed structure utilizes a four-coil inductive link for back telemetry, shared with a three-coil link for wireless power transmission. We propose a design procedure for geometrical optimization of the inductive link in terms of power transmission efficiency (PTE) considering specific absorption rate and data rate. We have designed a low-power pulse-based active data transmission circuit and characterized performance of the proposed inductive link in terms of its data rate and bit error rate (BER). The 1-mm 2 data-Tx/power-Rx coil is implemented using insulated bonding wire with diameter, resulting in measured PTE in tissue media of 2.01% at 131 MHz and 1.8-cm coil separation distance when the resonator coil inner radius is 1 cm. The measured BER at 1-Mbps data rate was and in the air and tissue environments, respectively.

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.

PubMed

Maishman, Luke; Obado, Samson O; Alsford, Sam; Bart, Jean-Mathieu; Chen, Wei-Ming; Ratushny, Alexander V; Navarro, Miguel; Horn, David; Aitchison, John D; Chait, Brian T; Rout, Michael P; Field, Mark C

2016-12-15

The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Recent progress and tests of radiation resistant impregnation materials for Nb3Sn coils

NASA Astrophysics Data System (ADS)

Bossert, R.; Krave, S.; Ambrosio, G.; Andreev, N.; Chlachidze, G.; Nobrega, A.; Novitski, I.; Yu, M.; Zlobin, A. V.

2014-01-01

Fermilab is collaborating with Lawrence Berkeley National Laboratory (LBNL) and Brookhaven National Laboratory (BNL) (US-LARP collaboration) to develop a large-aperture Nb3Sn superconducting quadrupole for the Large Hadron Collider (LHC) luminosity upgrade. An important component of this work is the development of materials that are sufficiently radiation resistant for use in critical areas of the upgrade. This paper describes recent progress in characterization of materials, including the baseline CTD101K epoxy, cyanate ester blends, and Matrimid 5292, a bismaleimide-based system. Structural properties of "ten stacks" of cable impregnated with these materials are tested at room and cryogenic temperatures and compared to the baseline CT-101K. Experience with potting 1 and 2 meter long coils with Matrimid 5292 are described. Test results of a single 1-m coil impregnated with Matrimid 5292 are reported and compared to similar coils impregnated with the traditional epoxy.

Hierarchical assembly of centriole subdistal appendages via centrosome binding proteins CCDC120 and CCDC68.

PubMed

Huang, Ning; Xia, Yuqing; Zhang, Donghui; Wang, Song; Bao, Yitian; He, Runsheng; Teng, Junlin; Chen, Jianguo

2017-04-19

In animal cells, the centrosome is the main microtubule-organizing centre where microtubules are nucleated and anchored. The centriole subdistal appendages (SDAs) are the key structures that anchor microtubules in interphase cells, but the composition and assembly mechanisms of SDAs are not well understood. Here, we reveal that centrosome-binding proteins, coiled-coil domain containing (CCDC) 120 and CCDC68 are two novel SDA components required for hierarchical SDA assembly in human cells. CCDC120 is anchored to SDAs by ODF2 and recruits CEP170 and Ninein to the centrosome through different coiled-coil domains at its N terminus. CCDC68 is a CEP170-interacting protein that competes with CCDC120 in recruiting CEP170 to SDAs. Furthermore, CCDC120 and CCDC68 are required for centrosome microtubule anchoring. Our findings elucidate the molecular basis for centriole SDA hierarchical assembly and microtubule anchoring in human interphase cells.

Wedge and spring assembly for securing coils in electromagnets and dynamoelectric machines

DOEpatents

Lindner, Melvin; Cottingham, James G.

1996-03-12

A wedge and spring assembly for use in electromagnets or dynamoelectric machines having a housing with an axis therethrough and a plurality of coils supported on salient poles that extend radially inward from the housing toward the housing axis to define a plurality of interpole spaces. The wedge and spring assembly includes a nonmagnetic retainer spring and a nonmagnetic wedge. The retainer spring is formed to fit into one of the interpole spaces, and has juxtaposed ends defining between them a slit extending in a direction generally parallel to the housing axis. The wedge for insertion into the slit provides an outwardly directed force on respective portions of the juxtaposed ends to expand the slit so that respective portions of the retainer spring engage areas of the coils adjacent thereto, thereby resiliently holding the coils against their respective salient poles. The retainer spring is generally triangular shaped to fit within the interpole space, and the wedge is generally T-shaped.

Wedge and spring assembly for securing coils in electromagnets and dynamoelectric machines

DOEpatents

Lindner, M.; Cottingham, J.G.

1996-03-12

A wedge and spring assembly for use in electromagnets or dynamoelectric machines is disclosed having a housing with an axis therethrough and a plurality of coils supported on salient poles that extend radially inward from the housing toward the housing axis to define a plurality of interpole spaces. The wedge and spring assembly includes a nonmagnetic retainer spring and a nonmagnetic wedge. The retainer spring is formed to fit into one of the interpole spaces, and has juxtaposed ends defining between them a slit extending in a direction generally parallel to the housing axis. The wedge for insertion into the slit provides an outwardly directed force on respective portions of the juxtaposed ends to expand the slit so that respective portions of the retainer spring engage areas of the coils adjacent thereto, thereby resiliently holding the coils against their respective salient poles. The retainer spring is generally triangular shaped to fit within the interpole space, and the wedge is generally T-shaped. 6 figs.

Model of vortex dynamics in superconducting films in two-coil measurements of the coherence length

NASA Astrophysics Data System (ADS)

Lemberger, Thomas; Loh, Yen Lee

In two-coil measurements on superconducting films, a magnetic field from a small coil is applied to the center of the film. When the amplitude of the ac field is increased, the film undergoes a transition from the ``Meissner'' state to a state with vortices and antivortices. Ultimately, the vortex density matches the applied magnetic field and field screening is negligible. Experimentally, the field at the transition is related to the superconducting coherence length, although a full theory of the relationship is lacking. We show that the mutual inductance between drive and pickup coils, on opposite sides of the film, as a function of ac field amplitude is well-described by a phenomenological model in which vortices and antivortices appear together in the film at the radius where the induced supercurrent is strongest, and then they move through a landscape of moderately strong vortex pinning sites. Work at OSU supported by DOE-Basic Energy Sciences through Grant No. FG02-08ER46533.

Initial Operation of the Nuclear Thermal Rocket Element Environmental Simulator

NASA Technical Reports Server (NTRS)

Emrich, William J., Jr.; Pearson, J. Boise; Schoenfeld, Michael P.

2015-01-01

The Nuclear Thermal Rocket Element Environmental Simulator (NTREES) facility is designed to perform realistic non-nuclear testing of nuclear thermal rocket (NTR) fuel elements and fuel materials. Although the NTREES facility cannot mimic the neutron and gamma environment of an operating NTR, it can simulate the thermal hydraulic environment within an NTR fuel element to provide critical information on material performance and compatibility. The NTREES facility has recently been upgraded such that the power capabilities of the facility have been increased significantly. At its present 1.2 MW power level, more prototypical fuel element temperatures nay now be reached. The new 1.2 MW induction heater consists of three physical units consisting of a transformer, rectifier, and inverter. This multiunit arrangement facilitated increasing the flexibility of the induction heater by more easily allowing variable frequency operation. Frequency ranges between 20 and 60 kHz can accommodated in the new induction heater allowing more representative power distributions to be generated within the test elements. The water cooling system was also upgraded to so as to be capable of removing 100% of the heat generated during testing In this new higher power configuration, NTREES will be capable of testing fuel elements and fuel materials at near-prototypic power densities. As checkout testing progressed and as higher power levels were achieved, several design deficiencies were discovered and fixed. Most of these design deficiencies were related to stray RF energy causing various components to encounter unexpected heating. Copper shielding around these components largely eliminated these problems. Other problems encountered involved unexpected movement in the coil due to electromagnetic forces and electrical arcing between the coil and a dummy test article. The coil movement and arcing which were encountered during the checkout testing effectively destroyed the induction coil in use at the time and resulted in NTREES being out of commission for a couple of months while a new stronger coil was procured. The new coil includes several additional pieces of support structure to prevent coil movement in the future. In addition, new insulating test article support components have been fabricated to prevent unexpected arcing to the test articles. Additional activities are also now underway to address ways in which the radial temperature profiles across test articles may be controlled such that they are more prototypical of what they would encounter in an operating nuclear engine. The causes of the temperature distribution problem are twofold. First, the fuel element test article is isolated in NTREES as opposed to being in the midst of many other mostly identical fuel elements in a nuclear engine. As a result, the fuel element heat flux boundary conditions in NTREES are far from adiabatic as would normally be the case in a reactor. Second, induction heating skews the power distribution such that power is preferentially deposited near the outside of the fuel element. Nuclear heating, conversely, deposits its power much more uniformly throughout the fuel element. Current studies are now looking at various schemes to adjust the amount of thermal radiation emitted from the fuel element surface so as to essentially vary the thermal boundary conditions on the test article. It is hoped that by properly adjusting the thermal boundary conditions on the fuel element test article, it may be possible to substantially correct for the inappropriate radial power distributions resulting from the induction heating so as to yield a more nearly correct temperature distribution throughout the fuel element.

A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments.

PubMed

Khachaturian, Mark Haig

2010-01-01

Awake monkey fMRI and diffusion MRI combined with conventional neuroscience techniques has the potential to study the structural and functional neural network. The majority of monkey fMRI and diffusion MRI experiments are performed with single coils which suffer from severe EPI distortions which limit resolution. By constructing phased array coils for monkey MRI studies, gains in SNR and anatomical accuracy (i.e., reduction of EPI distortions) can be achieved using parallel imaging. The major challenges associated with constructing phased array coils for monkeys are the variation in head size and space constraints. Here, we apply phased array technology to a 4-channel phased array coil capable of improving the resolution and image quality of full brain awake monkey fMRI and diffusion MRI experiments. The phased array coil is that can adapt to different rhesus monkey head sizes (ages 4-8) and fits in the limited space provided by monkey stereotactic equipment and provides SNR gains in primary visual cortex and anatomical accuracy in conjunction with parallel imaging and improves resolution in fMRI experiments by a factor of 2 (1.25 mm to 1.0 mm isotropic) and diffusion MRI experiments by a factor of 4 (1.5 mm to 0.9 mm isotropic).

A 4-channel 3 Tesla phased array receive coil for awake rhesus monkey fMRI and diffusion MRI experiments

PubMed Central

Khachaturian, Mark Haig

2010-01-01

Awake monkey fMRI and diffusion MRI combined with conventional neuroscience techniques has the potential to study the structural and functional neural network. The majority of monkey fMRI and diffusion MRI experiments are performed with single coils which suffer from severe EPI distortions which limit resolution. By constructing phased array coils for monkey MRI studies, gains in SNR and anatomical accuracy (i.e., reduction of EPI distortions) can be achieved using parallel imaging. The major challenges associated with constructing phased array coils for monkeys are the variation in head size and space constraints. Here, we apply phased array technology to a 4-channel phased array coil capable of improving the resolution and image quality of full brain awake monkey fMRI and diffusion MRI experiments. The phased array coil is that can adapt to different rhesus monkey head sizes (ages 4–8) and fits in the limited space provided by monkey stereotactic equipment and provides SNR gains in primary visual cortex and anatomical accuracy in conjunction with parallel imaging and improves resolution in fMRI experiments by a factor of 2 (1.25 mm to 1.0 mm isotropic) and diffusion MRI experiments by a factor of 4 (1.5 mm to 0.9 mm isotropic). PMID:21243106

Human RAD50 makes a functional DNA-binding complex.

PubMed

Kinoshita, Eri; van Rossum-Fikkert, Sari; Sanchez, Humberto; Kertokalio, Aryandi; Wyman, Claire

2015-06-01

The MRE11-RAD50-NBS1 (MRN) complex has several distinct functions in DNA repair including important roles in both non-homologous end-joining (NHEJ) and homologous recombination (HR). The biochemical activities of MR(N) have been well characterized implying specific functional roles for the components. The arrangement of proteins in the complex implies interdependence of their biochemical activities making it difficult to separate specific functions. We obtained purified human RAD50 and observed that it binds ATP, undergoes ATP-dependent conformational changes as well as having ATPase activity. Scanning force microscopy analysis clearly showed that RAD50 binds DNA although not as oligomers. RAD50 alone was not functional in tethering DNA molecules. ATP increased formation of RAD50 multimers which were however globular lacking extended coiled coils, in contrast to the MR complex where ATP induced oligomers have obvious coiled coils protruding from a central domain. These results suggest that MRE11 is important in maintaining the structural arrangement of RAD50 in the protein complex and perhaps has a role in reinforcing proper alignment of the coiled coils in the ATP-bound state. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

The accommodation index measures the perturbation associated with insertions and deletions in coiled‐coils: Application to understand signaling in histidine kinases

PubMed Central

Schmidt, Nathan W.; Grigoryan, Gevorg

2017-01-01

Abstract Coiled‐coils are essential components of many protein complexes. First discovered in structural proteins such as keratins, they have since been found to figure largely in the assembly and dynamics required for diverse functions, including membrane fusion, signal transduction and motors. Coiled‐coils have a characteristic repeating seven‐residue geometric and sequence motif, which is sometimes interrupted by the insertion of one or more residues. Such insertions are often highly conserved and critical to interdomain communication in signaling proteins such as bacterial histidine kinases. Here we develop the “accommodation index” as a parameter that allows automatic detection and classification of insertions based on the three dimensional structure of a protein. This method allows precise identification of the type of insertion and the “accommodation length” over which the insertion is structurally accommodated. A simple theory is presented that predicts the structural perturbations of 1, 3, 4 residue insertions as a function of the length over which the insertion is accommodated. Analysis of experimental structures is in good agreement with theory, and shows that short accommodation lengths give rise to greater perturbation of helix packing angles, changes in local helical phase, and increased structural asymmetry relative to long accommodation lengths. Cytoplasmic domains of histidine kinases in different signaling states display large changes in their accommodation lengths, which can now be seen to underlie diverse structural transitions including symmetry/asymmetry and local variations in helical phase that accompany signal transduction. PMID:27977891

Ophthalmic magnetic resonance imaging at 7 T using a 6-channel transceiver radiofrequency coil array in healthy subjects and patients with intraocular masses.

PubMed

Graessl, Andreas; Muhle, Maximilian; Schwerter, Michael; Rieger, Jan; Oezerdem, Celal; Santoro, Davide; Lysiak, Darius; Winter, Lukas; Hezel, Fabian; Waiczies, Sonia; Guthoff, Rudolf F; Falke, Karen; Hosten, Norbert; Hadlich, Stefan; Krueger, Paul-Christian; Langner, Soenke; Stachs, Oliver; Niendorf, Thoralf

2014-05-01

This study was designed to examine the feasibility of ophthalmic magnetic resonance imaging (MRI) at 7 T using a local 6-channel transmit/receive radiofrequency (RF) coil array in healthy volunteers and patients with intraocular masses. A novel 6-element transceiver RF coil array that makes uses of loop elements and that is customized for eye imaging at 7 T is proposed. Considerations influencing the RF coil design and the characteristics of the proposed RF coil array are presented. Numerical electromagnetic field simulations were conducted to enhance the RF coil characteristics. Specific absorption rate simulations and a thorough assessment of RF power deposition were performed to meet the safety requirements. Phantom experiments were carried out to validate the electromagnetic field simulations and to assess the real performance of the proposed transceiver array. Certified approval for clinical studies was provided by a local notified body before the in vivo studies. The suitability of the RF coil to image the human eye, optical nerve, and orbit was examined in an in vivo feasibility study including (a) 3-dimensional (3D) gradient echo (GRE) imaging, (b) inversion recovery 3D GRE imaging, and (c) 2D T2-weighted fast spin-echo imaging. For this purpose, healthy adult volunteers (n = 17; mean age, 34 ± 11 years) and patients with intraocular masses (uveal melanoma, n = 5; mean age, 57 ± 6 years) were investigated. All subjects tolerated all examinations well with no relevant adverse events. The 6-channel coil array supports high-resolution 3D GRE imaging with a spatial resolution as good as 0.2 × 0.2 × 1.0 mm, which facilitates the depiction of anatomical details of the eye. Rather, uniform signal intensity across the eye was found. A mean signal-to-noise ratio of approximately 35 was found for the lens, whereas the vitreous humor showed a signal-to-noise ratio of approximately 30. The lens-vitreous humor contrast-to-noise ratio was 8, which allows good differentiation between the lens and the vitreous compartment. Inversion recovery prepared 3D GRE imaging using a spatial resolution of 0.4 × 0.4 × 1.0 mm was found to be feasible. T2-weighted 2D fast spin-echo imaging with the proposed RF coil afforded a spatial resolution of 0.25 × 0.25 × 0.7 mm. This work provides valuable information on the feasibility of ophthalmic MRI at 7 T using a dedicated 6-channel transceiver coil array that supports the acquisition of high-contrast, high-spatial resolution images in healthy volunteers and patients with intraocular masses. The results underscore the challenges of ocular imaging at 7 T and demonstrate that these issues can be offset by using tailored RF coil hardware. The benefits of such improvements would be in positive alignment with explorations that are designed to examine the potential of MRI for the assessment of spatial arrangements of the eye segments and their masses with the ultimate goal to provide imaging means for guiding treatment decisions in ophthalmological diseases.

Highly sensitive current sensor utilizing CrNi-wire supported microfiber coils

NASA Astrophysics Data System (ADS)

Xie, Xiaodong; Li, Jie; Sun, Li-Peng; Jin, Long; Guan, Bai-ou

2013-09-01

High current sensitivity is obtained based on a microfiber that is wrapping around a chrome-nickel (CrNi) wire. Due to the strong heating effect of the CrNi wire with the flowing electric current, the mode index and the loop length of microfiber are changed, resulting in the shift of resonant wavelength. The measured current responsivity is as high as 220.65nm/A2, which is in two or three magnitude orders than the previously-obtained ones. We study the influence of component size to the structure performance, which is useful for future applications of current sensing or tuning devices.