bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of the complex between trypanosomal triosephosphate isomerase and N‐hydroxy‐4‐phosphono‐butanamide: Binding at the active site despite an “open” flexible loop conformation
Authors: Verlinde Christophe L.M.J. , Witmans Cornelis J. , Pijning Tjaard , Kalk Kor H. , Hol Wim G.J. , Callens Mia , Opperdoes Fred R. 
Published: February 2009

AbstractThe structure of triosephosphate isomerase from Trypanosoma brucei complexed with the competitive inhibitor N‐hydroxy‐4‐phosphono‐butanamide was determined by X‐ray crystallography to a resolution of 2.84 å. Full occupancy binding of the inhibitor is observed only at one of the active sites of the homodimeric enzyme where the flexible loop is locked in a completely open conformation by crystal contacts. There is evidence that the inhibitor also binds to the second active site of the enzyme, but with low occupancy. The hydroxamyl group of the inhibitor forms hydrogen bonds to the side chains of Asn 11, Lys 13, and His 95, whereas each of its three methylene units is involved in nonpolar interactions with the side chain of the flexible loop residue Ile 172. Interactions between the hydroxamyl and the catalytic base Glu 167 are absent. The binding of this phosphonate inhibitor exhibits three unusual features: (1) the flexible loop is open, in contrast with the binding mode observed in eight other complexes between triosephosphate isomerase and various phosphate and phosphonate compounds; (2) compared with these complexes the present structure reveals a 1.5‐å shift of the anion‐binding site; (3) this is the first phosphonate inhibitor that is not forced by the enzyme into an eclipsed conformation about the P‐CH2 bond. The results are discussed with respect to an ongoing drug design project aimed at the selective inhibition of glycolytic enzymes of T. brucei.
A 1H NMR study of a ternary peptide complex that mimics the interaction between troponin C and troponin I
Authors: Slupsky Carolyn M. , Shaw Gary S. , Campbell A. Patricia , Sykes Brian D. 
Published: February 2009

AbstractThe troponin I peptide Nα‐acetyl TnI (104–115) amide (TnIp) represents the minimum sequence necessary for inhibition of actomyosin ATPase activity of skeletal muscle (Talbot, J.A. & Hodges, R.S., 1981, J. Biol. Chem. 256, 2798–3802; Van Eyk, J.E. & Hodges, R.S., 1988, J. Biol. Chem. 263, 1726–1732; Van Eyk, J.E., Kay, C.M., & Hodges, R.S., 1991, Biochemistry 30, 9974–9981). In this study, we have used 1H NMR spectroscopy to compare the binding of this inhibitory TnI peptide to a synthetic peptide heterodimer representing site III and site IV of the C‐terminal domain of troponin C (TnC) and to calcium‐saturated skeletal TnC. The residues whose 1H NMR chemical shifts are perturbed upon TnIp binding are the same in both the site III/site IV heterodimer and TnC. These residues include F102, I104, F112, I113, I121, I149, D150, F151, and F154, which are all found in the C‐terminal domain hydrophobic pocket and antiparallel β‐sheet region of the synthetic site III/site IV heterodimer and of TnC. Further, the affinity of TnIp binding to the heterodimer (Kd = 192 + 37 μM) was found to be similar to TnIp binding to TnC (48 + 18 μM [Campbell, A.P., Cachia, P.J., & Sykes, B.D., 1991, Biochem. Cell Biol. 69, 674–681]). The results indicate that binding of the inhibitory region of TnI is primarily to the C‐terminal domain of TnC. The results also indicate how well the synthetic peptide heterodimer mimics the C‐terminal domain of TnC in structure and functional interactions.
Functional mapping of the surface of escherichia coli ribose‐binding protein: Mutations that affect chemotaxis and transport
Authors: Binnie1 R. Alan , Zhang Huide , Mowbray Sherry , Hermodson Mark A. 
Published: February 2009

AbstractRibose‐binding protein is a bifunctional soluble receptor found in the periplasm of Escherichia coli. Interaction of liganded binding protein with the ribose high affinity transport complex results in the transfer of ribose across the cytoplasmic membrane. Alternatively, interaction of liganded binding protein with a chemotactic signal transducer, Trg, initiates taxis toward ribose. We have generated a functional map of the surface of ribose‐binding protein by creating and analyzing directed mutations of exposed residues. Residues in an area on the cleft side of the molecule including both domains have effects on transport. A portion of the area involved in transport is also essential to chemotactic function. On the opposite face of the protein, mutations in residues near the hinge are shown to affect chemotaxis specifically.
Engineered plant phosphorylase showing extraordinarily high affinity for various α‐glucan molecules
Authors: Mori Hiroyuki , Tanizawa Katsuyuki , Fukui Toshio 
Published: February 2009

Abstractα‐Glucan phosphorylases are characterized by considerable difference in substrate specificities, even though the primary structures are well conserved among the enzymes from microorganisms, plants, and animals. The higher plant phosphorylase isozyme designated as type L exhibits low affinity for a large, highly branched glucan (glycogen), presumably due to steric hindrance caused by a unique 78‐residue insertion located beside the mouth of the active‐site cleft, whereas another isozyme without the insertion (designated as type H) shows very high affinity for both linear and branched glucans. Using the recombinant type L isozyme from potato tuber as a starting framework and aiming at altering its substrate specificity, we have genetically engineered the 78‐residue insertion and its flanking regions. Firstly, removal of the insertion and connection of the newly formed C‐ and N‐terminals yielded a totally inactive enzyme, although the protein was produced in Escherichia coli cells in a soluble form. Secondly, a chimeric phosphorylase, in which the 78‐residue insertion and its flanking regions are replaced by the corresponding region of the type H isozyme, has been shown to exhibit high affinity for branched glucans (Mori, H., Tanizawa, K., & Fukui, T., 1993, J. Biol. Chem. 268, 5574–5581), but when two and four unconserved residues in the N‐terminal flanking region of the chimeric phosphorylase were mutated back to those of the type L isozyme, the resulting mutants showed significantly lowered affinity for substrates. Finally, a chimeric phosphorylase, in which a 112‐residue sequence of the rabbit muscle enzyme involving the glycogen‐storage site was substituted for the 78‐residue insertion and its flanking regions of the type L isozyme, showed extraordinarily high affinity for a variety of substrates including not only large, branched glucans but also small, linear ones.
Sites of iodination in recombinant human brain‐derived neurotrophic factor and its effect on neurotrophic activity
Authors: Rosenfeld Robert , Philo John S. , Haniu Mitsuru , Stoney Kendall , Rohde Michael F. , Wu Gay‐May , Narhi Linda O. , Wong Caroline , Boone Tom , Hawkins Nessa N. , Miller James M. , Arakawa Tsutomu 
Published: February 2009

AbstractRecombinant human brain‐derived neurotrophic factor (BDNF) is now under extensive investigation because of its potential clinical applications. Radioactively labeled proteins are usually required to study receptor binding and pharmacokinetic properties of proteins. This study was undertaken to see if iodination affects the biological and conformational properties of a recombinant BDNF. BDNF was iodinated using a stoichiometric amount of nonradioactive cold NaI to minimize multiple iodinations. Of the four tyrosines present in BDNF–Tyr‐52, Tyr‐54, Tyr‐63, and Tyr‐86–only Tyr‐63 and Tyr‐86 were iodinated under the experimental conditions used. Iodination of Tyr‐63 resulted in modification without alteration of the biological activity, whereas iodination of Tyr‐86 resulted in a molecule with highly compromised biological activity. Similar inactivation was observed if both Tyr‐63 and Tyr‐86 were iodinated. These modified proteins exhibited conformation and dimerization apparently identical to those of the native protein, as demonstrated by analytical ultracentrifugation, gel filtration, light scattering, and circular dichroism. From these results, we concluded that Tyr‐52 and Tyr‐54 are not accessible to the reagent and are probably buried in the hydrophobic core, whereas Tyr‐63 and Tyr‐86 are exposed on the surface of the molecule; of the two exposed residues, only Tyr‐86 contributes to the biological activity.
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
Authors: Sheffler Will , Baker David 
Published: February 2009

AbstractWe present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high‐resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.
Central quadrant procurement of radical prostatectomy specimens
Authors: Morrison Carl , Cheney Richard , Johnson Candace S. , Smith Gary , Mohler James L. 
Published: February 2009

AbstractObtaining high quality fresh or frozen prostate tissue in gram amounts promotes the research of prostate cancer. Due to the inability to effectively recognize prostate cancer upon the cut section of a fresh prostate many pathology departments perform whole organ processing precluding the procurement of prostate tissue. Some sites randomly procure tissue, while others perform specialized procedures that can be difficult to duplicate. Neither of these types of procurement consistently results in gram quantities of tissue procured from each prostate with a high percentage of samples yielding tissue corresponding to cancer. In this study, we present a simplified model of prostate tissue procurement that has no impact on Gleason grade, tumor stage or margin status, requires minimal specialized processing, and obtains gram amounts of fresh tissue from each radical prostatectomy specimen with a high percentage yielding cancer tissue. Prostate 69: 770–773, 2009. © 2009 Wiley‐Liss, Inc.
Multistep filling of porous silicon with conductive polymer by electropolymerization
Authors: Fukami Kazuhiro , Sakka Tetsuo , Ogata Yukio H. , Yamauchi Takeshi , Tsubokawa Norio 
Published: February 2009

AbstractThe filling of porous silicon with polypyrrole by electropolymerization was investigated. The filling with polypyrrole proceeded preferentially along the porous silicon wall, leading to the formation of tubular structures. By repeating the porosification, the pore filling and the additional porosification, through‐tubes of polypyrrole were formed in macropores. The technique to form through‐tube was also applied to medium‐sized pores. A double layer with polypyrrole was produced by the repetition of porosification and pore filling twice. The immobilization of glucose oxidase was performed by electropolymerization in an aqueous solution containing glucose oxidase and pyrrole. Glucose oxidase was immobilized physically in the polypyrrole film. In the double layer, the sensitivity of glucose oxidase was measured by electrochemical oxidation of hydrogen peroxide, which was produced by the enzymatic reaction of glucose oxidase to gluconolactone. When glucose oxidase was immobilized in the upper layer, glucose was detected sensitively. On the other hand, when glucose oxidase was immobilized in the lower layer, the sensing current showed a slow and a low response. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of initial conditions and growth temperature on the properties of nonpolar a ‐plane AlN grown by LP‐HVPE
Authors: Wu Jie‐Jun , Katagiri Yusuke , Okuura Kazuki , Li Da‐Bing , Miyake Hideto , Hiramatsu Kazumasa 
Published: February 2009

AbstractAlN was grown on r ‐ and c ‐plane sapphire substrates by low‐pressure hydride vapor phase epitaxy (LP‐HVPE). Nitridation and buffer methods were used and compared. Results show that the buffer method is appropriate for the growth of a‐plane AlN. In‐plane stresses were measured and found to be different in the two in‐plane directions parallel and perpendicular to the AlN c‐axis. In‐plane stress anisotropy is reduced at high temperature leading to a smoother surface, partly owing to a decreased difference in the growth rates between two in‐plane directions. However, too high a temperature decreases the crystal quality of a‐plane AlN. Thus, there exists an optimal temperature range for the growth of a‐plane AlN, in which improved crystal and surface qualities can both be obtained. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polarization effect on electronic band structure of InGaN/GaN multi‐quantum wells
Authors: Song Hooyoung , Kim Jin Soak , Kim Eun Kyu , Suh Moon Suhk , Seo Yong Gon , Hwang Sung‐Min 
Published: February 2009

AbstractWe have characterized the effect of piezoelectric field in strained InGaN/GaN multi‐quantum wells (MQWs) by using the deep level transient spectroscopy (DLTS). The photoluminescence peak of the quantum wells was observed at 2.612 eV roughly matched with DLTS results. And the carrier profile obtained by the relation of capacitance‐voltage showed carrier accumulation peaks representing the quantum wells. The thermal activation energy calculated from DLTS spectra decreased by about 0.12 eV with increasing the reverse bias field. This energy shift can be explained by the partial compensation of the internal piezoelectric field. In this report, we suggested the DLTS technique as a useful method to characterize the quantum confined Stark effect in InGaN/GaN MQWs structure. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
InGaN light emitting diodes for 415 nm–520 nm spectral range by plasma assisted MBE
Authors: Siekacz M , Szańkowska M. Ł. , Feduniewicz‐Zmuda A. , Smalc‐Koziorowska J. , Cywiński G. , Grzanka S. , Wasilewski Z. R. , Grzegory I. , Łucznik B. , Porowski S. , Skierbiszewski C. 
Published: February 2009

AbstractIn this work we study the growth of the Light Emitting Diodes (LEDs) by Plasma Assisted MBE (PAMBE). The active LEDs region was grown to cover the spectral range spanning from 415 nm to 520 nm. We demonstrate efficient LEDs with the highest optical power output of 1.5 mW and 20 mA for 415 nm. For longer wavelengths we observe a drop of the optical power. The reduction of the quantum efficiency for green emission can be related to the presence of strong built‐in piezoelectric fields or increased number of nonradiative recombinarion centers. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
GaN‐based embedded 2D photonic crystal LEDs: Numerical optimization and device characterization
Authors: Matioli Elison , Iza Michael , Choi Yong‐Seok , Wu Feng , Keller Stacia , Masui Hisashi , Hu Evelyn , Speck James , Weisbuch Claude 
Published: February 2009

AbstractWe present the numerical optimization of GaN‐based embedded 2D‐Photonic Crystal (PhC) LEDs based on a full 3D scattering matrix model pointing out the importance of a proper vertical design in embedded PhC structures. The growth of such structures following the numerical simulation trends is shown to be feasible. Experimental results of a bright embedded 2D‐PhC LED (9mW at 20mA) under electrical injection are reported. Angular measurements are performed to understand the efficiency in light extraction of the PhCs and the mechanisms limiting its full potential are presented. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
One‐ and two‐dimensional porous silicon photonic crystals: momentum dispersion relations and stopbands analysis
Authors: Gutman Nadav , Lubarski David , Sa'ar Amir 
Published: February 2009

AbstractWe report on a novel approach to analyze and measure the optical properties of one‐ and two ‐dimensional photonic crystals (PCs) in all spatial directions inlcluding the symmetry axis of the PCs. The analysis is based on calculating momentum dispersion relations between the ordinary and the Bloch components of the wavevector and finding momentum stop‐bands of the PC. This method provides a direct way to analyze the angular dependence of the reflection and the diffraction pattern of a monochromatic optical beam approaching the PC. Measurements have been performed on 1D PCs, e.g., 1D periodic structures of micro‐porous silicon and 2D periodic arrays of macro‐porous silicon. The periodicity of these PCs is about 2.5 to 4 μm so that their momentum stop‐bands fall in the mid‐infrared (IR) wavelengths. We analyze several geometries, including slabs and prisms, to map the momentum dispersion relations and stopbands associated with guided and radiation modes. Angular reflection and diffraction measurements using a tunable CO2 laser showed a good agreement with the calculated momentum dispersion relations. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A comparison of formulas for the design of cumulative sum control charts
Authors: Cox M. A. A. 
Published: February 2009

AbstractA conventional cumulative sum control chart has a V‐mask where each arm makes an angle θ with the horizontal and has a lead distance d. These parameters are usually related to h (=dA tan(ϑ), A is a scaling factor) and k(=A tan(ϑ)). Two systems of formulas are examined for derivinghandkfor selected values of the in control and out of control average run lengths. This is the first time an exhaustive comparison has been made. Copyright © 2009 John Wiley & Sons, Ltd.
A Bayesian zero‐failure reliability demonstration test of high quality electro‐explosive devices
Authors: Fan Tsai‐Hung , Chang Chia‐Chen 
Published: February 2009

AbstractUsually, for high reliability products the production cost is high and the lifetime is much longer, which may not be observable within a limited time. In this paper, an accelerated experiment is employed in which the lifetime follows an exponential distribution with the failure rate being related to the accelerated factor exponentially. The underlying parameters are also assumed to have the exponential prior distributions. A Bayesian zero‐failure reliability demonstration test is conducted to design forehand the minimum sample size and testing length subject to a certain specified reliability criterion. Probability of passing the test design as well as predictive probability for additional experiments is also derived. Sensitivity analysis of the design is investigated by a simulation study. Copyright © 2009 John Wiley & Sons, Ltd.
Direct dynamics study on the mechanism and the kinetics of the reaction of CH3NH2 with OH
Authors: Tian Wei , Wang Wenliang , Zhang Yue , Wang Weina 
Published: February 2009

AbstractA theoretical study of the mechanism and the kinetics for the hydrogen abstraction reaction of methylamine by OH radical has been presented at the CCSD(T)/6‐311 ++G(2d,2p)//CCSD/6‐31G(d) level of theory. Our theoretical calculations suggest a stepwise mechanism involving the formation of a prereactant complex in the entrance channel and a preproduct complex in the exit channel, for the two hydrogen abstraction channels involving the methyl and amine groups. For clarity, the diagram of potential for the reaction is given. The calculated standard reaction enthalpies are −98.48 and −76.50 kJ mol−1 and barrier heights are 0.36 and 25.25 kJ mol−1, respectively. The rate constants are evaluated by means of the improved canonical variational transition state theory with small‐curvature tunneling correction (ICVT/SCT) in the temperature range of 299–3000 K. The calculated results show that the rate constants at experimentally measured temperatures are in good agreement with the experimental values. It is shown that the calculated rate constants exhibit a non‐Arrhenius behavior. Moreover, the variational effect is obvious in the calculated temperature range. The dominant product channel is to form CH2NH2 and H2O via hydrogen abstraction from the CH3 group of CH3NH2 by OH in the calculated temperature range. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
A feedback suppression algorithm for reliable satellite multicast based on spatial–temporal prediction of the satellite channel
Authors: Anastasopoulos Markos P. , Panagopoulos Athanasios D. , Cottis Panayotis G. 
Published: February 2009

AbstractThe major problem limiting the scalability of large‐scale multicast satellite networks is feedback implosion that arises whenever a large number of users simultaneously transmit feedback messages (FBMs) through the network, thus occupying a significant portion of satellite system resources. In satellite networks operating above 10 GHz, attenuation due to rain constitutes the dominant fading mechanism deteriorating the quality of service. In this paper, a novel scheme for providing large‐scale reliable multicast services through a star‐based geostationary satellite topology is presented incorporating accurate channel modeling of the propagation phenomena. The new protocol is based on the selection of an area representative that provides quick FBMs aiming at suppressing FBMs originating from the rest of the network users. The scheme provides a timely reaction to changes of either the channel conditions or the network topology by properly updating the selection of representatives. Through appropriate simulations, comparisons and examples it is demonstrated that the new approach suppresses FBMs very effectively. Copyright © 2009 John Wiley & Sons, Ltd.
Correcting for 3D distortion when using backscattered electron detectors in a scanning electron microscope
Authors: Proctor Jacob M. 
Published: February 2009

AbstractA variable pressure scanning electron microscope (VPSEM) can produce a topographic surface relief of a physical object under examination, in addition to its two‐dimensional (2D) image. This topographic surface relief is especially helpful when dealing with porous rock because it may elucidate the pore‐space structure as well as grain shape and size. Whether the image accurately reproduces the physical object depends on the management of the hardware, acquisition, and postprocessing. Two problems become apparent during testing: (a) a topographic surface relief of a precision ball bearing is distorted and does not correspond to the physical dimensions of the actual sphere and (b) an image of a topographic surface relief of a Berea sandstone is geometrically tilted and topographically distorted even after standard corrections are applied. The procedure presented here is to ensure the veracity of the image, and includes: (a) adjusting the brightness and contrast levels originally provided by the manufacturer and (b) tuning the amplifiers of the backscatter detector plates to be equal to each other, and producing zero voltage when VPSEM is idle. This procedure is tested and verified on the said two physical samples. SCANNING 31: 59–64, 2009. © 2009 Wiley Periodicals, Inc.