bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and measurement of 10 GHz oscillators with ultra‐low phase noise
Authors: Andrade L. A. , Aguiar O. D. , Mosso M. M. , Santos B. P. , Podcameni A.
Published: February 2009

This work describes the development of 10‐GHz feedback oscillators with ultra‐low phase noise. Measurement procedures involving injection locking, composition with synchronized sources and vibrational isolation are described. The application is for gravitational waves detectors. The phase‐noise performance obtained was −100 dBc/Hz at 3 kHz, which is still 45 dB worse than the goal performance. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1120–1126, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24239
Ultra‐wideband square slot antenna with a novel diamond open‐ended microstrip feed
Authors: Naser‐Moghadasi Mohammad , Koohestani Mohsen , Golpour Mohsen , Virdee Bal S.
Published: February 2009

A novel ultra‐wideband microstrip patch antenna is presented. The proposed antenna exhibits an impedance bandwidth of 127% over an ultra‐wideband frequency range from 2.9 to 13 GHz, which makes it an excellent candidate for UWB applications. Simulated results are compared with the fabricated antenna measured performance, which show good agreement. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1075–1080, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24242
A radio‐over‐fiber system with photonics generated OFDM signals by using directly modulated laser
Authors: Chen L. , Lu J. , He J. , Dong Z. , Wen S.
Published: February 2009

We have experimentally demonstrated a radio‐over‐fiber system transmitting 2.5 Gbt/s orthogonal frequency division multiplexing (OFDM) signals carried by 40 GHz millimetre ‐wave. The 40 GHz optical millimeter wave signals were generated by a directed modulation laser driven by the 2.5 Gb/s electrical OFDM signals carried by 20 GHz RF signals. The power penalty is less than 1 dB power penalty at bit error rate of 10−5 after transmission over 20 km standard single mode fiber. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 971–973, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24248
Multisection bandpass filters using capacitively loaded transmission lines
Authors: Li Zhen , Palmer William D. , Joines William T.
Published: February 2009

In the frequency range from 50 to 500 MHz, lumped element inductors may have internal resonances, and the distributed nature of the physical structure is solved using transmission‐line theory. Stub filters (shorted or opened stubs separated by sections of line) are quite reliable and easy to manufacture, but their physical size is a disadvantage at these frequencies. In this article, the size reduction process is illustrated by a series of design examples, starting with a bandpass filter at 200 MHz that uses half‐wavelength tapped‐stubs and has multiple resonant sections separated by quarter‐wavelength sections of transmission line. By using this technique the filter area is reduced from 243.67 square inches to 5.99 square inches, an impressive factor of about 40×! Theoretical results are verified by measurements. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1107–1112, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24252
Shifted SSOR preconditioning technique for electromagnetic wave scattering problems
Authors: Chen J. Q. , Liu Z. W. , Xu K. , Ding D. Z. , Fan Z. H. , Chen R. S.
Published: February 2009

To efficiently solve large dense complex linear system arising from electric field integral equations (EFIE) formulation of electromagnetic scattering problems, the multilevel fast multipole method (MLFMM) is used to accelerate the matrix‐vector product operations. The symmetric successive over‐relaxation (SSOR) preconditioner is constructed based on the near‐field matrix of the EFIE and employed to speed up the convergence rate of iterative methods. This technique can be greatly improved by shifting the near‐field matrix of the EFIE with the principle value term of the magnetic field integral equation (MFIE) operator. Numerical results demonstrate that this method can reduce both the number of iterations and the computational time significantly with low cost for construction and implementation of preconditioners. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1035–1039, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24254
Dual band‐notched ultra‐wideband antenna with codirectional SRR
Authors: Wang Wentao , Gong Shuxi , Cui Zhen , Liu Jianfu , Ling Jin
Published: February 2009

In this article, a rectangular monopole ultra‐wideband antenna with dual band‐notched characteristic is proposed. The bandstop characteristic is produced by a new configuration of split ring resonators (SRRs). Being different from the conventional reverse split rings, this novel structure consists of two codirectional split rings and locates in the both sides of the rectangular radiating patch. Furthermore, the length of each ring controls the corresponding resonant frequency. By adjusting the dimension of the codirectional SRRs, the band‐rejected frequencies from 3.25 to 3.75 GHz and from 5.15 to 5.6 GHz can be achieved easily. These rejected bands cover the operating bands, which have been applied to WiMAX and WLAN. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1032–1034, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24255
A novel planar multimode bandpass filter with radial perturbation
Authors: Ma Kaixue , Yeo Kiat Seng , Sun Qiang
Published: February 2009

A novel multimode bandpass filter with good rejection band is proposed by using a radial stub. The radial stub cannot only perturb the traditional resonator for the multimode operation but also generate additional zero point at the stopband for the stopband control. With proper input/output coupling, additional two poles, that is, four poles, can be achieved for the proposed filter structure. The experimental results of the four‐mode filter show low insertion loss, good stopband performance, and compact size. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 964–966, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24258
Erratum: A graphical tool for analysis and design of bi‐characteristic‐impedance transmission lines
Authors: Torrungrueng D. , Chou P. Y. , Krairiksh M.
Published: February 2009

Originally published in Microwave Opt Technol Lett 49: 2368–2372, 2007. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1154, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24260
Compact low pass filter using novel elliptic shape DGS
Authors: Chen XiaoQun , Wang LingXia , Weng LiHong , Shi XiaoWei
Published: February 2009

A novel elliptic shape defected ground structure (DGS) is investigated for low pass filter (LPF) applications. An equivalent RLC circuit model is presented and its corresponding parameters are also extracted from the measured S‐parameters. The filter presents the advantages of compact size, high selectivity, low insertion loss and high out‐band suppression more than 32 dB from 5.15 to 10 GHz. Good agreements with response of equivalent circuit, electromagnetic simulation, and measurement is demonstrated. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1088–1091, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24263
Sensitivity analysis of the effective parameter extraction procedure for metamaterial applications
Authors: Tyagi Varun , Semouchkina Elena
Published: February 2009

We examine the accuracy of metamaterial effective parameters extraction from the reflection and transmission data and show that this procedure could lead to significant errors in the effective permittivity and permeability values near frequencies where the reflection coefficient has low magnitudes, while the refractive index can still be accurately extracted. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1013–1017, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24267
Dispersion in one‐dimensional photonic band gap periodic transmission lines
Authors: Angert C. Isaac , Remillard S. K.
Published: February 2009

Dispersion in periodic microstrip transmission lines was investigated by using S‐parameters to calculate the characteristic impedance and the complex propagation constant. Dispersion curves determined from a variety of methods, including simulation with IE3D and measurement with a network analyzer, were compared with an analytic transcendental model providing self‐consistent validation of each method. Simulated S‐parameters agreed with measurement, including the case of a multi‐layered substrate. Very similar dispersion curves were produced using simulated S‐parameters, simulated current distributions, analytic calculation and measured S‐parameters. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1010–1013, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24268
Complement 3 deficiency impairs early pregnancy in mice
Authors: Chow Wang‐Ngai , Lee Yin‐Lau , Wong Po‐Chau , Chung Man‐Kin , Lee Kai‐Fai , Yeung William Shu‐Biu
Published: February 2009

Human oviductal cells produce complement‐3 (C3) and its derivative, iC3b. These molecules are important in immune responses. Our recent study suggested that iC3b also possessed embryotrophic activity and it stimulates the blastulation and hatching rates of in vitro cultured mouse embryos. The objective is to study the impact of C3 deficiency on early pregnancy in vivo using homozygous C3‐deficient (C3KO) and wild‐type (C3WT) mice. C3 protein was undetectable in the reproductive tissues of C3KO mice. Deficiency in C3 is associated with significantly longer estrous cycle (P = 0.037). No significant difference was found in the ovulation rate, total cell count in blastocysts and implantation rate between the wild‐type and the C3KO mice, though C3KO mice tended to have lower values in the latter two parameters. On day 15 of pregnancy, C3KO mice had fewer conceptus (P < 0.001) and higher resorption rate (P < 0.001) than that of C3WT mice. The fetal and placental weights (P < 0.001) were lower in the C3KO mice. The placenta of C3KO mice had smaller spongiotrophoblast (P = 0.001) and labyrinth (P = 0.037). Deficiency in C3 is associated with mild impairment in early pregnancy including longer estrous cycle and higher resorption rates after implantation. The impairment may be related to compromised placental development leading to under‐developed fetuses. Mol. Reprod. Dev. 76: 647–655, 2009. © 2009 Wiley‐Liss, Inc.
Recursive algorithms for unbalanced banded Toeplitz systems
Authors: Favati P. , Lotti G. , Menchi O.
Published: February 2009

Direct recursive algorithms for the solution of band Toeplitz systems are considered here. They exploit the displacement rank properties, which allow a large reduction of computational efforts and storage requirements. Their use of the Sherman–Morrison–Woodbury formula turns out to be particularly suitable for the case of unbalanced bandwidths. The computational costs of the algorithms under consideration are compared both in a theoretical and practical setting. Some stability issues are discussed as well. Copyright © 2009 John Wiley & Sons, Ltd.
Randomized controlled trial of SPIRIT: An effective approach to preparing African‐American dialysis patients and families for end of life
Authors: Song Mi‐Kyung , Ward Sandra E. , Happ Mary Beth , Piraino Beth , Donovan Heidi S. , Shields Anne‐Marie , Connolly Mary C.
Published: February 2009

This randomized controlled trial tested an intervention, Sharing Patients' Illness Representations to Increase Trust (SPIRIT), designed to enhance communication regarding end‐of‐life care between African Americans with end‐stage renal disease (ESRD) and their chosen surrogate decision makers (N = 58 dyads). We used surveys and semi‐structured interviews to determine the feasibility, acceptability, and preliminary effects of SPIRIT on patient and surrogate outcomes at 1 week and 3 months post‐intervention. We also evaluated patients' deaths and surrogates' end‐of‐life decision making to assess surrogates' perceptions of benefits and limitations of the SPIRIT while facing end‐of‐life decisions. We found that SPIRIT promoted communication between patients and their surrogates and was effective and well received by the participants. © 2009 Wiley Periodicals, Inc. Res Nurs Health 32:260–273, 2009
Teacher expectations on the directiveness continuum in consultation
Authors: Tysinger P. Dawn , Tysinger Jeffrey A. , Diamanduros Terry
Published: February 2009

The study investigated the consultation approaches of collaborative‐directive and collaborative‐nondirective and the influence of teacher expectations for consultation on their ratings of consultation success. Teachers viewed videotaped consultation sessions of a collaborative‐directive or collaborative‐nondirective consultation session that either matched or mismatched their expectations. The study found significantly higher ratings for the consultants and interventions when the collaborative‐directive approach was used. In addition, teachers in conditions that matched their expectations for consultation rated consultants and interventions significantly higher than did teachers in mismatched conditions. The importance of this line of research lies in its practical application, allowing practitioners of consultation and trainers of school psychologists greater knowledge in selection of the appropriate consultation approach to maximize perceived consultant effectiveness and intervention acceptability. © 2009 Wiley Periodicals, Inc.
Methods for measuring student response to stimulant medication: A meta‐analytic review
Authors: Someki Fumio , Burns Matthew K.
Published: February 2009

Measuring student response to interventions has become an important role for school psychologists. Children with Attention‐Deficit/Hyperactivity Disorder (ADHD) are frequently treated with stimulant medication, but the response to the treatment is rarely adequately assessed. The current study examined the sensitivity of measures used to assess the outcomes of stimulant medication for children identified with ADHD using meta‐analytic procedures. A total of 812 articles were reviewed with 35 being selected for the study based on a common treatment protocol of .3 to .5 mg/kg with a 2‐ to 8‐week pre‐ and post‐test interval. Measures were categorized as behavioral, psychological, or physiological. A total of 81 effect sizes were computed with a total unbiased estimate of effect of .53 and unbiased estimates of effect of .11 for physiological measures, .38 for psychological measures, and .56 for behavioral measures. Tests of homogeneity found nonsignificant results within each of the three categories. © 2009 Wiley Periodicals, Inc.
Functional colloidal particles stabilized by layered silicate with hydrophilic face and hydrophobic polymer brushes
Authors: Wu Yani , Zhang Jian , Zhao Hanying
Published: February 2009

In this study, we describe a new strategy for producing narrowly dispersed functional colloidal particles stabilized by a nanocomposite with hydrophilic clay faces and hydrophobic polystyrene (PS) brushes on the edges. This method involves preparation of polymer brushes on the edges of clay layers and Pickering suspension polymerization of styrene in the presence of the nanocomposites. PS brushes on the edges of clay layers were prepared by atom transfer radical polymerization. X‐ray diffraction and thermogravimetric analysis results indicated that PS chains were grafted to the edges of clay platelets. Transmission electron microscope results showed that different morphologies of clay‐PS particles could be obtained in different solvents. In water, clay‐PS particles aggregated together, in which PS chains collapsed forming nanosized hydrophobic domains and hydrophilic clay faces stayed in aqueous phase. In toluene, clay‐PS particles formed face‐to‐face structure. Narrowly dispersed PS colloidal particles stabilized by clay‐PS were prepared by suspension polymerization. Because of the negatively charged clay particles on the surface, the zeta potential of the PS colloidal particles was negative. Positively charged poly(2‐vinyl pyridine) (P2VP) chains were adsorbed to the surface of PS colloidal particles in aqueous solution at a low pH value, and gold nanoparticles were prepared in P2VP brushes. Such colloidal particles may find important applications in a variety of fields including waterborne adhesives, paints, catalysis of chemical reactions, and protein separation. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1535–1543, 2009
Synthesis, photoluminescence, and electrochromism of novel aromatic poly(amine‐1,3,4‐oxadiazole)s bearing anthrylamine chromophores
Authors: Yen Hung‐Ju , Liou Guey‐Sheng
Published: February 2009

Two novel poly(amine‐hydrazide)s were prepared from the polycondensation reactions of the dicarboxylic acid, 9‐[N,N‐di(4‐carboxyphenyl)amino]anthracene (1), with terephthalic dihydrazide (TPH) and isophthalic dihydrazide (IPH) via the Yamazaki phosphorylation reaction, respectively. The poly(amine‐hydrazide)s were readily soluble in many common organic solvents and could be solution cast into transparent films. Differential scanning calorimetry (DSC) indicated that these hydrazide polymers had glass‐transition temperatures (Tg) in the range of 182–230 °C and could be thermally cyclodehydrated into the corresponding oxadiazole polymers in the range of 300–400 °C. The resulting poly(amine‐1,3,4‐oxadiazole)s had useful levels of thermal stability associated with high Tg (263–318 °C), 10% weight‐loss temperatures in excess of 500 °C, and char yield at 800 °C in nitrogen higher than 55%. These organo‐soluble anthrylamine‐based poly(amine‐hydrazide)s and poly (amine‐1,3,4‐oxadiazole)s exhibited maximum UV‐vis absorption at 346–349 and 379–388 nm in N‐methyl‐2‐pyrrolidone (NMP) solution, respectively. Their photoluminescence spectra in NMP solution showed maximum bands around 490–497 nm in the green region. The poly(amine‐hydrazide) I‐IPH showed a green photoluminescence at 490 nm with PL quantum yield of 29.9% and 17.0% in NMP solution and film state, respectively. The anthrylamine‐based poly(amine‐1,3,4‐oxadiazole)s revealed a electrochromic characteristics with changing color from the pale yellow neutral form to the red reduced form when scanning potentials negatively from 0.00 to −2.20 V. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1584–1594, 2009
Synthesis of dendritic terpolymers consisting of polystyrene, polybutadiene, and polyisoprene with different isomerisms
Authors: Rangou Sofia , Avgeropoulos Apostolos
Published: February 2009

We report the synthesis of two 2nd generation dendritic terpolymers consisting of poly(butadiene) (PB) of 1,4 geometric isomerism, poly(isoprene) (PI) enriched in 3,4 geometric isomerism (at least 55% PI3,4) and polystyrene (PS). The main focus of this work was the synthesis of well‐defined dendritic terpolymers exhibiting high levels of molecular and compositional homogeneity. The preparation of these materials was achieved via anionic polymerization techniques in combination with chlorosilane linking chemistry. The molecular characterization of the intermediate products and the final dendritic materials was accomplished via gel permeation chromatography, membrane osmometry, differential scanning calorimetry, and 1H‐nuclear magnetic resonance spectroscopy, leading to the conclusion that they can be considered model polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1567–1574, 2009
Preparation and properties of conductive silver/photosensitive polyimide nanocomposites
Authors: Li Tung‐Lin , Hsu Steve Lien‐Chung
Published: February 2009

A new electrically conductive photoresist has been developed. It is based on the dispersion of silver nanoflakes in a negative‐tone photosensitive polyimide (PSPI) precursor. 2‐Mercaptopropionic acid was used as the surfactant to modify the silver nanoflake surface for the dispersion of silver nanoflakes in the polymer. The silver/PSPI nanocomposites showed electrical conductivity at a low silver content of 10 wt %. The electrical conductivity of the silver/PSPI nanocomposites ranged from 10 to 104 S/cm, which was dependent on the silver weight fraction in the resist formulation. Patterns with a resolution of 30 μm were obtained from the silver/PSPI nanocomposites. The silver/PSPI nanocomposites had excellent thermal properties. Their glass transition temperatures were above 360 °C and thermal decomposition temperatures were over 420 °C. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1575–1583, 2009
The effects of airway closure in central apneas and obstructed respiratory efforts in mixed apneas in preterm infants
Authors: Al‐Sufayan F. , Bamehrez M. , Kwiatkowski K. , Alvaro R.E.
Published: February 2009

Background

Airway closure during central apnea could allow for better gas exchange. However, the return of inspiratory efforts against a closed airway may cause greater desaturation and prolongation of apnea.

Objective

To investigate the effect of patency of the airway and obstructed respiratory efforts on the length of apneas and the degree and slope of O2 desaturation and bradycardia.

Methods

All mixed apneas observed in 15 preterms were matched 1:2 with the longest central apneas in each infant. Central apneas were further classified using the amplified cardiac airflow oscillation in those with airway open and in those with airway closed.

Results

No differences were found in the length of apnea, slope of O2 desaturation, delay between the onset of apnea and onset of desaturation, lowest post‐apneic SpO2, and time of recovery of SpO2 between central apneas with and without airway closure. Although mixed apneas were significantly longer than central apneas, their initial central component was significantly shorter than the length of central apneas. In mixed apneas, the onset of O2 desaturation occurred faster, SpO2 decreased lower, and recovered slower compared with central apneas. The slope of O2 desaturation after the obstructed respiratory efforts was significantly greater than before the obstructed respiratory efforts.

Conclusions

In preterm infants: (1) airway closure during central apneas does not limit oxygen desaturation; (2) respiratory efforts against a closed airway prolong apnea and worsen the degree of desaturation and bradycardia. Although respiratory efforts are not necessary to induce airway closure, inspiratory efforts against a closed airway could trigger inhibitory cardio‐respiratory responses causing significant desaturation, bradycardia, and prolongation of apnea. Pediatr Pulmonol. 2009; 44:253–259. © 2009 Wiley‐Liss, Inc.
MMP‐9 and TIMP‐1 in the cord blood of premature infants developing BPD
Authors: Fukunaga Shinnosuke , Ichiyama Takashi , Maeba Shinji , Okuda Masayuki , Nakata Masahiko , Sugino Norihiro , Furukawa Susumu
Published: February 2009

We investigated matrix metalloproteinase‐9 (MMP‐9) and tissue inhibitor of metalloproteinase 1 (TIMP‐1) levels in the cord blood of 29 premature infants who were <30 weeks gestation. One, 8, and 14 infants developed severe, moderate and mild bronchopulmonary dysplasia (BPD), respectively, and 6 did not. MMP‐9 and TIMP‐1 levels in the cord blood were determined by ELISA. MMP‐9/TIMP‐1 ratios in the cord blood of infants who developed severe or moderate BPD (n = 9) were significantly higher than those who developed mild BPD or did not develop BPD (n = 20; P = 0.015). Multivariate linear regressions demonstrated that MMP‐9 levels and MMP‐9/TIMP‐1 ratios in the cord blood of the premature infants correlated with the oxygen supplementation period (r = 0.58, P = 0.003 and r = 0.41, P = 0.030, respectively). The MMP‐9 levels and MMP‐9/TIMP‐1 ratios correlated with the severity of maternal chorioamnionitis (both trend P = 0.006).

The MMP‐9 levels and MMP‐9/TIMP‐1 ratios in the cord blood may be related to the pathogenesis and severity of BPD and maternal chorioamnionitis. Pediatr Pulmonol. 2009; 44:267–272. © 2009 Wiley‐Liss, Inc.
Exploiting genomic patterns to discover new supramolecular protein assemblies
Authors: Beeby Morgan , Bobik Thomas A. , Yeates Todd O.
Published: February 2009

Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat‐shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data.
Crystal structure of checkpoint kinase 2 in complex with NSC 109555, a potent and selective inhibitor
Authors: Lountos George T. , Tropea Joseph E. , Zhang Di , Jobson Andrew G. , Pommier Yves , Shoemaker Robert H. , Waugh David S.
Published: February 2009

Checkpoint kinase 2 (Chk2), a ser/thr kinase involved in the ATM‐Chk2 checkpoint pathway, is activated by genomic instability and DNA damage and results in either arrest of the cell cycle to allow DNA repair to occur or apoptosis if the DNA damage is severe. Drugs that specifically target Chk2 could be beneficial when administered in combination with current DNA‐damaging agents used in cancer therapy. Recently, a novel inhibitor of Chk2, NSC 109555, was identified that exhibited high potency (IC50 = 240 nM) and selectivity. This compound represents a new chemotype and lead for the development of novel Chk2 inhibitors that could be used as therapeutic agents for the treatment of cancer. To facilitate the discovery of new analogs of NSC 109555 with even greater potency and selectivity, we have solved the crystal structure of this inhibitor in complex with the catalytic domain of Chk2. The structure confirms that the compound is an ATP‐competitive inhibitor, as the electron density clearly reveals that it occupies the ATP‐binding pocket. However, the mode of inhibition differs from that of the previously studied structure of Chk2 in complex with debromohymenialdisine, a compound that inhibits both Chk1 and Chk2. A unique hydrophobic pocket in Chk2, located very close to the bound inhibitor, presents an opportunity for the rational design of compounds with higher binding affinity and greater selectivity.
Backbone structure of a small helical integral membrane protein: A unique structural characterization
Authors: Page Richard C. , Lee Sangwon , Moore Jacob D. , Opella Stanley J. , Cross Timothy A.
Published: February 2009

The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three‐dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C‐terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 Å rmsd backbone structure with a transmembrane domain defined at 0.40 Å. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long‐range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins.
Effect of trehalose on protein structure
Authors: Jain Nishant Kumar , Roy Ipsita
Published: February 2009

Trehalose is a ubiquitous molecule that occurs in lower and higher life forms but not in mammals. Till about 40 years ago, trehalose was visualized as a storage molecule, aiding the release of glucose for carrying out cellular functions. This perception has now changed dramatically. The role of trehalose has expanded, and this molecule has now been implicated in a variety of situations. Trehalose is synthesized as a stress‐responsive factor when cells are exposed to environmental stresses like heat, cold, oxidation, desiccation, and so forth. When unicellular organisms are exposed to stress, they adapt by synthesizing huge amounts of trehalose, which helps them in retaining cellular integrity. This is thought to occur by prevention of denaturation of proteins by trehalose, which would otherwise degrade under stress. This explanation may be rational, since recently, trehalose has been shown to slow down the rate of polyglutamine‐mediated protein aggregation and the resultant pathogenesis by stabilizing an aggregation‐prone model protein. In recent years, trehalose has also proved useful in the cryopreservation of sperm and stem cells and in the development of a highly reliable organ preservation solution. This review aims to highlight the changing perception of the role of trehalose over the last 10 years and to propose common mechanisms that may be involved in all the myriad ways in which trehalose stabilizes protein structures. These will take into account the structure of trehalose molecule and its interactions with its environment, and the explanations will focus on the role of trehalose in preventing protein denaturation.
Parallel screening and optimization of protein constructs for structural studies
Authors: Rasia Rodolfo M. , Noirclerc‐Savoye Marjolaine , Bologna Nicolás G. , Gallet Benoit , Plevin Michael J. , Blanchard Laurence , Palatnik Javier F. , Brutscher Bernhard , Vernet Thierry , Boisbouvier Jérôme
Published: February 2009

A major challenge in structural biology remains the identification of protein constructs amenable to structural characterization. Here, we present a simple method for parallel expression, labeling, and purification of protein constructs (up to 80 kDa) combined with rapid evaluation by NMR spectroscopy. Our approach, which is equally applicable for manual or automated implementation, offers an efficient way to identify and optimize protein constructs for NMR or X‐ray crystallographic investigations.
Amino acid sequence of fibrolase, a direct‐acting fibrinolytic enzyme from agkistrodon contortrix contortrix venom
Authors: Randolph Anne , Chamberlain Scott H. , Chu H.‐L. Cathy , Masiarz Frank R. , Retzios Anastassios D. , Markland Francis S.
Published: February 2009

The complete amino acid sequence of fibrolase, a fibrinolytic enzyme from southern copperhead (Agkistrodon contortrix contortrix) venom, has been determined. This is the first report of the sequence of a direct‐acting, non‐hemorrhagic fibrinolytic enzyme found in snake venom. The majority of the sequence was established by automated Edman degradation of overlapping peptides generated by a variety of selective cleavage procedures. The amino‐terminus is blocked by a cyclized glutamine (pyroglutamic acid) residue, and the sequence of this region of the molecule was determined by mass spectrometry. Fibrolase is composed of 203 residues in a single polypeptide chain with a molecular weight of 22,891, as determined by the sequence. Its sequence is homologous to the sequence of the hemorrhagic toxin Ht‐d of Crotalus atrox venom and with the sequences of two metalloproteinases from Trimeresurus flavoviridis venom. Microheterogeneity in the sequence was found at both the amino‐terminus and at residues 189 and 192. All six cysteine residues in fibrolase are involved in disulfide bonds. A disulfide bond between cysteine‐118 and cysteine‐198 has been established and bonds between cysteines‐158/165 and between cysteines‐160/192 are inferred from the homology to Ht‐d. Secondary structure prediction reveals a very low percentage of α‐helix (4%), but much greater β‐structure (39.5%). Analysis of the sequence reveals the absence of asparagine‐linked glycosylation sites defined by the consensus sequence: asparagine‐X‐serine/threonine.
Mutation of conserved residues in Escherichia coli thioredoxin: Effects on stability and function
Authors: Gleason Florence K.
Published: February 2009

Mutations were made in three highly conserved residues in Escherichia coli thioredoxin. An internal charged residue, Asp‐26, was changed to an alanine. The mutant protein was more stable than the wild type. It can function as a substrate for thioredoxin reductase with a 10‐fold increase in the Km over the wild type. Although the redox potential was not substantially changed from that of the wild type, thioredoxin D26A was a poor reducing agent for ribonucleotide reductase. Asp‐26 apparently serves to maintain an optimal charge distribution in the active site region for interaction with other proteins. Mutation of a surface Pro‐34 in the active site disulfide ring to a serine had little effect on protein stability. A slight decrease in the redox potential (9 mV) made thioredoxin P34S a better reducing agent for ribonucleotide reductase. In contrast, mutation of the internal cis Pro‐76 to an alanine destabilized the protein. The data indicate a change had also occurred in the charge distribution in the active site region. Thioredoxin P76A had a higher redox potential than the wild type protein and was not an effective reducing agent for ribonucleotide reductase. It was concluded that this residue is essential for maintaining the conformation of the active site and the redox potential of thioredoxin.
Optical activity associated with the sulfur to metal charge transfer bands of Zn and Cd GAL4
Authors: Basile Lena A. , Coleman Joseph E.
Published: February 2009

The N‐terminal DNA‐binding domain of the GAL4 transcription factor, isolated as a proteolytic fragment of 63 amino acid residues, GAL4(63), or cloned as a 62‐residue subdomain, GAL4(62*), binds 2 Cd(II) ions. Both Cd derivatives show intense ellipticity bands associated with ‐S− → Cd charge transfer bands at 250 nm (+), 233 nm (‐), and 218 nm (+). Molar ellipticity values are (5–7) x 104 deg · cm2 · dmol−1. The energies and pattern (+, ‐, +) of these ellipticity bands are similar to those observed for the Cd(II) clusters of metallothionein. The latter are believed to be due to the presence of bridging cysteine ligands (Willner, H.W., Vasak, M., & Kägi, J.H.R., 1987, Biochemistry 26, 6287–6292). Circular dichroism provides further evidence that the GAL4 DNA‐binding domain forms a binuclear Cd cluster with the amino acid sequence ‐C11‐X2‐C14‐X6‐C21‐X6‐C28‐X2‐C31‐X6‐C38‐found in GAL4(62*). Zn2GAL4(62*) has much weaker ellipticity associated with the higher energy ‐S− → Zn charge transfer bands. Removal of the metal ions from GAL4(62*) results in substantial changes in the near UV circular dichroism due to both loss of the charge transfer bands and changes in the conformation of the peptide backbone. Binding of the UASG enhancer DNA element to either Zn or Cd GAL4(62*) alters the ellipticity of the ‐S− → metal charge transfer bands suggesting that DNA binding is associated with some changes in conformation around the metal cluster.
Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin β4
Authors: Sippl Manfred J. , Hendlich Manfred , Lackner Peter
Published: February 2009

Recently we developed methods for the construction of knowledge‐based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three‐dimensional models of polypeptide chains.

The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model.

The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X‐ray analysis and thymosin β4, a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.
Thermodynamics of melittin tetramerization determined by circular dichroism and implications for protein folding
Authors: Wilcox William , Eisenberg David
Published: February 2009

The tetramerization of melittin, a 26‐amino acid peptide from Apis mellifera bee venom, has been studied as a model for protein folding. Melittin converts from a monomeric random coil to an α‐helical tetramer as the pH is raised from 4.0 to 9.5, as ionic strength is increased, as temperature is raised or lowered from about 37 °C, or as phosphate is added. The thermodynamics of this tetramerization (termed “folding”) are explored using circular dichroism. The melittin tetramer has two pKa values of 7.5 and 8.5 corresponding to protonation of the N‐terminus and Lys 23, respectively. pKa values calculated with the program DelPhi (Gilson, M.K., Sharp, K.A., & Honig, B.H., 1987, J. Comp. Chem. 9, 327–335; Gilson, M.K. & Honig, B.H., 1988a, Proteins3, 32–52; Gilson, M.K. & Honig, B.H., 1988b, Proteins 4, 7–18) agree with experimental titration data. Greater electrostatic repulsion of these protonated groups destabilizes the tetramer by 3.6 kcal/mol at pH 4.0 compared to pH 9.5. Increasing the concentration of NaCl in the solution from 0 to 0.5 M stabilizes the tetramer by 5–6 kcal/mol at pH 4.0. The effect of NaCl is modeled with a ligand‐binding approach. The melittin tetramer is found to have a temperature of maximum stability ranging from 35.5 to 43 °C depending on the pH, unfolding above and below that temperature. ΔCp0 for folding ranges from –0.085 to –0.102 cal g−1 K−1 comparable to that of other small globular proteins (Privalov, P.L., 1979, Adv. Protein Chem. 33, 167–241). ΔH0 and ΔS0 are found to decrease with temperature, presumably due to the hydrophobic effect (Kauzmann, W., 1959, Adv. Protein Chem. 14, 1–63). Phosphate is found to perturb the equilibrium substantially with a maximal effect at 150 mM, stabilizing the tetramer at pH 7.4 and 25 °C by 4.6 kcal/mol. The enthalpy change due to addition of phosphate (–7.5 kcal/mol at 25 °C) can be accounted for by simple dielectric screening. Both circular dichroism and crystallographic results suggest that phosphate may bind Lys 23 at the ends of the elongated tetramer. These detailed measurements give insight into the relative importance of various forces for the stability of melittin in the folded form and may provide an experimental standard for future tests of computational energetics on this simple protein system.
A proposed link between nitrogen and carbon metabolism involving protein phosphorylation in bacteria
Authors: Reizer Jonathan , Reizer Aiala , Saier Milton H. , Jacobson Gary R.
Published: February 2009

We demonstrate that certain phosphoryl transfer proteins of the bacterial phosphotransferase system (PTS), the fructose‐ and mannitol‐specific IIA proteins or domains, are homologous to a class of proteins, one of which is known to affect transcription of some of the nitrogen‐regulatory σ54‐dependent operons in Klebsiella pneumoniae. The phosphorylatable histidyl residue in the homologous PTS proteins and the consensus sequence in the vicinity of the active‐site histidine are fully conserved in all members that comprise this family of proteins. A phylogenetic tree of the eight protein members of this family was constructed, and a “signature” sequence that can serve for the identification of new protein members of this family is proposed. These observations suggest that PTS‐catalyzed protein phosphorylation may provide a regulatory link between carbon and nitrogen assimilation in bacteria.
Electrostatic interactions in the association of proteins: An analysis of the thrombin–hirudin complex
Authors: Karshikov Andrej , Bode Wolfram , Tulinsky Alexander , Stone Stuart R.
Published: February 2009

The role of electrostatic interactions in stabilization of the thrombin–hirudin complex has been investigated by means of two macroscopic approaches: the modified Tanford–Kirkwood model and the finite‐difference method for numerical solution of the Poisson–Boltzmann equations. The electrostatic potentials around the thrombin and hirudin molecules were asymmetric and complementary, and it is suggested that these fields influence the initial orientation in the process of the complex formation. The change of the electrostatic binding energy due to mutation of acidic residues in hirudin has been calculated and compared with experimentally determined changes in binding energy. In general, the change in electrostatic binding energy for a particular mutation calculated by the modified Tanford–Kirkwood approach agreed well with the experimentally observed change. The finite‐difference approach tended to overestimate changes in binding energy when the mutated residues were involved in short‐range electrostatic interactions. Decreases in binding energy caused by mutations of amino acids that do not make any direct ionic interactions (e.g., Glu 61 and Glu 62 of hirudin) can be explained in terms of the interaction of these charges with the positive electrostatic potential of thrombin. Differences between the calculated and observed changes in binding energy are discussed in terms of the crystal structure of the thrombin–hirudin complex.
The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X‐ray structures
Authors: Hyberts Sven G. , Goldberg Matthew S. , Havel Timothy F. , Wagner Gerhard
Published: February 2009

A high‐precision solution structure of the elastase inhibitor eglin c was determined by NMR and distance geometry calculations. A large set of 947 nuclear Overhauser (NOE) distance constraints was identified, 417 of which were quantified from two‐dimensional NOE spectra at short mixing times. In addition, a large number of homonuclear 1H‐1H and heteronuclear 1H‐15N vicinal coupling constants were used, and constraints on 42 χ1 and 38 ϕ angles were obtained. Structure calculations were carried out using the distance geometry program DG‐II. These calculations had a high convergence rate, in that 66 out of 75 calculations converged with maximum residual NOE violations ranging from 0.17 Å to 0.47 Å. The spread of the structures was characterized with average root mean square deviations () between the structures and a mean structure. To calculate the  unbiased toward any single structure, a new procedure was used for structure alignment. A canonical structure was calculated from the mean distances, and all structures were aligned relative to that. Furthermore, an angular order parameter S was defined and used to characterize the spread of structures in torsion angle space. To obtain an accurate estimate of the precision of the structure, the number of calculations was increased until the  and the angular order parameters stabilized. This was achieved after approximately 40 calculations. The structure consists of a well‐defined core whose backbone deviates from the canonical structure ca. 0.4 Å, a disordered N‐terminal heptapeptide whose backbone deviates by 0.8–12 Å, and a proteinase‐binding loop whose backbone deviates up to 3.0 Å. Analysis of the angular order parameters and inspection of the structures indicates that a hinge‐bending motion of the binding loop may occur in solution. Secondary structures were analyzed by comparison of dihedral angle patterns. The high precision of the structure allows one to identify subtle differences with four crystal structures of eglin c determined in complexes with proteinases.
Functional interactions of ligand cofactors with Escherichia coli transcription termination factor rho. I. Binding of ATP
Authors: Geiselmann Johannes , Von Hippel Peter H.
Published: February 2009

Escherichia coli transcription termination factor rho is an RNA‐dependent ATPase, and ATPase activity is required for all its functions. We have characterized the binding of ATP to the physiologically relevant hexameric association state of rho in the absence of RNA and have shown that there are six ATP binding sites per rho hexamer. This stoichiometry has been verified by a number of different techniques, including ultracentrifugation, ultrafiltration, and fluorescence titration studies. We have also shown that ATP can bind to isolated monomers of rho when the hexamer is dissociated with the mild denaturant myristyltrimethylammonium bromide, demonstrating that each protomer of rho carries an ATP binding site. The six binding sites that we observe in the rho hexamer are not equivalent; the hexamer contains three strong (Ka ≈︁ 3 × 106 M−1) and three weak (Ka ≈︁ 105 M−1) binding sites for ATP. The binding constant of the weak binding sites is just the reciprocal of the enzymatic Km for ATP as a substrate; thus these weak sites, as well as the strong sites, can, in principle, take part in the catalytic cycle. The asymmetry induced (or manifested) by ATP binding reduces the symmetry of the rho hexamer from a D3 to a pseudo‐D3 state. This “breakage” of symmetry has implications for the molecular mechanism of rho, because an asymmetric structure can lead to directional helicase activity by invoking directionally distinct RNA binding and release reactions (see Geiselmann, J., Yager, T.D., & von Hippel, P.H., 1992c, Protein Sci. 1, 861–873).