bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance analysis of a printed super‐wideband antenna
Authors: Dong Yuandan , Hong Wei , Liu Leilei , Zhang Yan , Kuai Zhenqi
Published: February 2009

Performance in both frequency‐domain and time‐domain for a printed super‐wideband antenna is studied and presented in this article. The proposed antenna consists of a corner‐rounded ground plane, a tapered microstrip feeder and a novel radiating patch which is made by one half‐disc and one half‐ellipse. This configuration allows to implement a ratio impedance bandwidth more than 25:1 for voltage standing wave ratio (VSWR) < 2. Critical antenna characteristics including antenna transfer function, group delay and time‐domain pulse responses are experimentally investigated and analyzed in detail by setting up a transceiving antenna system, which give designers a thorough understanding and useful information about antenna performance and application it exhibits behind the extremely broad bandwidth. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 949–956, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24222
Ultra wideband pulse generation using microstrip coupled lines
Authors: Tekin Ibrahim
Published: February 2009

In this article, a novel ultra wideband (UWB) pulse generator using microstrip coupled lines (MCL) is described. The MCL circuit generates an UWB pulse which can used both in UWB communication transmitter and receiver circuits as well as ground penetrating and wall through radars. The proposed circuit formed by microstrip coupled lines and terminations generates an UWB pulse from one of the output of the microstrip couple lines. Different bandwidth pulses from the circuit can be obtained by adjusting the length of the microstrip lines. An example circuit is implemented on an FR4 substrate with dielectric constant of εr = 4.6. The length of the microstrip line was set to 9.3 cm, and pulse duration of 235 ps is obtained. This corresponds to a Gaussian pulse with 4.3 GHz bandwidth at the center frequency of 2.15 GHz. Time and frequency measurements results are presented for time waveform and |S21| of the circuit, respectively. The circuit is low cost and can be easily implemented for UWB applications. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 944–949, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24223
Chip‐inductor‐embedded small‐size printed strip monopole for WWAN operation in the mobile phone
Authors: Kang Ting‐Wei , Wong Kin‐Lu
Published: February 2009

A simple small‐size printed strip monopole embedded with a chip inductor for covering all the five operating bands of GSM850/900/1800/1900/UMTS for wireless wide area network (WWAN) operation in the mobile phone is presented. The antenna consists of a chip‐inductor‐embedded longer radiating strip and a shorter radiating strip. With a 10‐nH chip inductor embedded, the longer radiating strip has a length of about 46 mm only (about 0.14 wavelength at 900 MHz), yet supports a wide resonant mode at about 900 MHz for the antenna's lower band to cover GSM850/900 operation. The shorter radiating strip has a length of about 30 mm (about 0.2 wavelength at 2000 MHz) and provides a wide resonant mode at about 2000 MHz for the antenna's upper band to cover GSM1800/1900/UMTS operation. With the five operating bands covered, the two radiating strips occupy a small printed area of about 350 mm2 on the system circuit board of the mobile phone. Details of the proposed antenna are described, and the specific absorption rate results of the antenna are also analyzed. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 966–971, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24225
Design of dual‐band SIR bandpass filter with a broad upper rejection band for WLANs
Authors: Chang Yu‐Chi , Kao Chia‐Hsiung , Weng Min‐Hang
Published: February 2009

In this letter, we proposed the design of novel dual‐band bandpass filter (BPF) with a broad upper rejection band using only two asymmetric stepped impedance resonators (SIRs), which has a smaller circuit size in comparison of previous works. The feature of the asymmetric SIR is only one‐step discontinuity, which is different from the conventional SIR with two‐step discontinuities. By selecting properly the impedance ratio (R) and physical length ratio (α) of the proposed asymmetric SIRs, the low loss dual‐band BPF centered at 2.4/5.2 GHz with a wide upper rejection band from 6 to 14 GHz can be implemented perfectly. The bandwidths and the coupling coefficients of the two passbands can be tunable by adjusting the coupling gap distance between the resonators, which are calculated by using full‐wave simulator IE3D. Good agreement between the electromagnetic (EM) simulation and measurement is reported. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1143–1146, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24227
A low local oscillator power K‐band mixer based on tunneling diodes
Authors: Magrini Iacopo , Cidronali Alessandro , Manes Gianfranco
Published: February 2009

In this article, we will demonstrate a low local oscillator (LO) power K‐band mixer based on a tunneling diode technology. Due to its unique diode characteristics, no DC supply is needed, whereas an LO power as low as −2 dBm is required for nominal functionality. The energy‐efficient MMIC prototype integrates a pair of heterojunction interband tunnel diodes and a 90° coplanar broadband coupler. The prototype is optimized within the 19–26 GHz band, with an IF ranging from zero to 7 GHz. In addition, when compared with other mixers, it has the lowest LO power requirement with a conversion loss ranging from 6 to 10 dB, an input compression point of −3 dBm and an intercept 2nd and 3rd order intermodulation point of 22 and 12 dBm, respectively. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1140–1143, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24228
Millimeter‐wave transition of coplanar line to substrate‐integrated LiNbO3 waveguide for traveling‐wave electro‐optical modulator
Authors: Mortazy Ebrahim , Xu Feng , Meunier Michel , Wu Ke
Published: February 2009

In this article, a transition of coplanar line to substrate‐integrated waveguide onto electro‐optical LiNbO3 substrate for the design of traveling‐wave optical phase modulator at 60 GHz were proposed, designed, and fabricated for the first time. Micromachining of the LiNbO3 substrate, which is transparent to a wide range of laser wavelengths, was done by using Excimer laser. Metallized via holes around the coplanar line are considered for the purpose of mode suppression. Also, a cavity resonator was designed to increase the circuit bandwidth. Measurement results show about 5 GHz bandwidth for the demonstrated substrate‐integrated electro‐optical waveguide. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1105–1107, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24229
A low‐power low‐phase‐noise 48‐GHz CMOS LC VCO for 60‐GHz dual‐conversion receiver
Authors: Chang Tien‐Hung , Chen Chang‐Zhi , Lin Yo‐Sheng , Huang Guo‐Wei
Published: February 2009

In this article, a low‐power low‐phase‐noise 48‐GHz CMOS LC voltage‐control oscillator (VCO) using standard 0.13‐μm CMOS technology is reported. Low‐power consumption is achieved by maximizing the equivalent parallel resistance of the LC tank, while low‐phase‐noise is achieved by suppressing the up‐conversion of the flicker noise of the PMOS current source to 1/f3‐shaped phase noise close to the carrier. The VCO dissipated 5.556 mW power, and achieved state‐of‐the‐art phase noise of −105 dBc/Hz at 1‐MHz offset from 47.85 GHz. The corresponding figure‐of‐merit (FOM) was −191.1 dBc/Hz, which is better than those of the reported CMOS LC VCOs around 48 GHz in the literature. The chip area was 0.94 × 0.9 mm2including the test pads. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 997–1000, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24256
Design of a microstip fed step slot antenna for UWB communication
Authors: Gopikrishna M. , Krishna Deepti Das , Aanandan C. K. , Mohanan P. , Vasudevan K.
Published: February 2009

The design and performance of a stepped slot printed monopole antenna in the ultrawideband is presented in this article. Multiple resonances generated by the stepped slot geometry are matched in the ultrawideband using a modified microstrip feed. The impedance bandwidth (SWR < 2) of the antenna is from 3 to 11 GHz. Radiation patterns are stable and omnidirectional with appreciable gain throughout the band. Performance of the antenna is also analyzed in the time domain, which reveals good pulse handling capabilities. Compact geometry of the antenna allows easy commercial deployment. © 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1126–1129, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.24262
Mono‐ and difluorinated 1,1,2,2,9,9,10,10‐octafluoro[2.2]paracyclophanes (AF4s)—A 1H and 19F NMR study
Authors: Ghiviriga Ion , Dulong Florian , Dolbier William R.
Published: February 2009

Complete assignment of the 1H and 19F chemical shifts in 4‐fluoro‐AF4 (1) were based on the nOes seen in its 19F‐1H HOESY spectrum. This allowed for identification of features which can further be applied to the assignment of the regiochemistry of substituted perfluoroparacyclophanes (PCPs) and AF4s: (i) an aromatic fluorine couples with the two fluorines in the closest bridge that are syn to it, with constants of ca. 20 Hz; (ii) an aromatic fluorine couples with the bridge fluorine five bonds away that is anti to it in the same paraphenylene moiety, with a constant of ca. 3.5 Hz; (iii) the geminal coupling of the bridge fluorines is 246 Hz if they have an ortho fluorine and 238 Hz if they do not; (iv) a bridge fluorine couples with those aromatic protons in the same paraphenylene moiety that are four or five bonds away and anti. These features have been used to assign the regiochemistry of the pseudo‐ortho, pseudo‐meta and pseudo‐para‐difluoro AF4s 2–4. It has also been demonstrated that SCS for the bridge fluorines can be used as well for this assignment. Copyright © 2009 John Wiley & Sons, Ltd.
High‐field head radiofrequency volume coils using transverse electromagnetic (TEM) and phased array technologies
Authors: Avdievich Nikolai I. , Hetherington Hoby P.
Published: February 2009

This article describes technological advances in quadrature transverse electromagnetic (TEM) volume coils and phased arrays reported recently from our laboratory developed for MRI and MRS imaging of the human brain. The first part of this work presents a new method for tuning TEM volume coils based on measurements of the radiofrequency current distribution in the coil elements. This technique facilitates bench adjustment of the coils' homogeneity and is particularly important for tuning double‐tuned TEM volume coils. We have also used this method to optimize other TEM configurations such as a quadrature TEM half‐volume coil and a split TEM coil. TEM half‐volume coils provide greater sensitivity over localized regions than conventional full‐volume coils, and the split TEM coil provides greater patient access and ease of use. The second part of this work describes the development of single‐tuned and double‐tuned transmit TEM volume coils in combination with phased arrays. A variety of different techniques for active detuning of single‐tuned and double‐tuned TEM volume coils are presented along with the development of phased arrays and transmission line preamplifier decoupling. The final section describes the use of counter rotating current (CRC) surface coils in phased arrays. Because of the intrinsic isolation of CRC coils from transmit volume coils, CRC arrays can be used simultaneously with volume coils for both reception and transmission. Near the center of the human head where both the phased array and the volume coil produce similar sensitivities, simultaneous reception enhances the signal‐to‐noise ratio. Conversely, simultaneous transmission can be used to boost the transmit field in peripheral brain regions from the volume coil to provide a more homogeneous transmit field. Copyright © 2009 John Wiley & Sons, Ltd.
Preconditioners for ill‐posed Toeplitz matrices with differentiable generating functions
Authors: Estatico C.
Published: February 2009

Both theoretical analysis and numerical experiments in the literature have shown that the Tyrtyshnikov circulant superoptimal preconditioner for Toeplitz systems can speed up the convergence of iterative methods without amplifying the noise of the data. Here we study a family of Tyrtyshnikov‐based preconditioners for discrete ill‐posed Toeplitz systems with differentiable generating functions. In particular, we show that the distribution of the eigenvalues of these preconditioners has good regularization features, since the smallest eigenvalues stay well separated from zero. Some numerical results confirm the regularization effectiveness of this family of preconditioners. Copyright © 2009 John Wiley & Sons, Ltd.
Degradable star polymers with high “click” functionality
Authors: Wiltshire James T. , Qiao Greg G.
Published: February 2009

Degradable polyester‐based star polymers with a high level of functionality in the arms were synthesized via the “arms first” approach using an acetylene‐functional block copolymer macroinitiator. This was achieved by using 2‐hydroxyethyl 2′‐methyl‐2′‐bromopropionate to initiate the ring‐opening polymerization (ROP) of caprolactone monomer followed by an atom transfer radical polymerization (ATRP) of a protected acetylene monomer, (trimethylsilyl)propargyl methacrylate. The hydroxyl end‐group of the resulting block copolymer macroinitiator was subsequently crosslinked under ROP conditions using a bislactone monomer, 4,4′‐bioxepanyl‐7,7′‐dione, to generate a degradable core crosslinked star (CCS) polymer with protected acetylene groups in the corona. The trimethylsilyl‐protecting groups were removed to generate a CCS polymer with an average of 1850 pendent acetylene groups located in the outer block segment of the arms. The increased functionality of this CCS polymer was demonstrated by attaching azide‐functionalized linear polystyrene via a copper (I)‐catalyzed cycloaddition reaction between the azide and acetylene groups. This resulted in a CCS polymer with “brush‐like” arm structures, the grafted segment of which could be liberated via hydrolysis of the polyester star structure to generate molecular brushes. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1485–1498, 2009
Amphiphilic block copolymers containing thermally degradable poly(phthalaldehyde) blocks
Authors: Köstler Stefan , Zechner Barbara , Trathnigg Bernd , Fasl Hubert , Kern Wolfgang , Ribitsch Volker
Published: February 2009

In this study, the preparation of a new class of amphiphilic block copolymers consisting of a poly(phthalaldehyde) (PPA) block and hydrophilic poly(alkylene oxide) blocks is described. PPA was prepared by ionic cyclopolymerization. A telechelic polymer block was prepared by endcapping of the PPA by a bifunctional reagent carrying isocyanate and isothiocyanate groups. As the second block, monoamino‐terminated poly(alkylene oxide)s (Surfonamines®, also known as Jeffamines®) were chosen. These polymers could be readily coupled to the PPA telechel and gave amphiphlic, mainly ABA‐type block copolymers. The PPA block of these products can be selectively depolymerized at moderate temperature. The block copolymers were characterized by dual‐detection size exclusion chromatography, and the defined and stepwise thermal decomposition of the two different block types were shown by thermogravimetric analysis. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1499–1509, 2009
Anionic polymerization of methacrylates by samarium (III) enolate on networked polystyrene: Effects of its sterically confined environment on polymerization behavior
Authors: Nagai Daisuke , Fujii Asuka , Tanaka Masayoshi , Ochiai Bungo , Sudo Atsushi , Endo Takeshi
Published: February 2009

Anionic polymerization of methacrylates under sterically confined environment in a spherical beads‐shaped networked polystyrene (NwPS) matrix is described. The initiator used herein is a samarium (Sm) (III) enolate, which was formed by treatment of 2‐bromoisobutylate immobilized in the side chain of NwPS with Sm (II) iodide. By using this NwPS‐bound initiator, polymerization of a series of methacrylates (=solid‐supported polymerization) was studied to find its two aspects: (1) In the early stages, the rate constant for each methacrylate was comparable to that for its conventional solution‐phase polymerization using a Sm (III) enolate, suggesting that methacrylate can be efficiently supplied to the propagating end by its free permeation without any interference by the networked structure of the matrix. (2) After the early stages, the rate constant decreased remarkably, implying that permeation of methacrylate was sterically interfered by the formed poly(methacrylate) that filled the confined space in NwPS, as supported by a SEM image of the resulting beads, of which pores were filled with the formed polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1510–1521, 2009
Synthesis of polymeric nanocapsules with a crosslinked shell through interfacial miniemulsion polymerization
Authors: Cao Zhihai , Shan Guorong
Published: February 2009

A water‐soluble comonomer, N‐isopropylacrylamide (NIPAM), and an oil‐soluble crosslinker, divinylbenzene (DVB), have been combined in a system for the synthesis of nanocapsules with crosslinked shells through interfacial miniemulsion polymerization by encapsulating a liquid nonsolvating hydrocarbon. Oligomers of poly(N‐isopropylacrylamide) (PNIPAM) were dehydrated and separated from the aqueous phase and were adsorbed by the nanodroplets or latex particles and then anchored at their interfaces by means of a crosslinking reaction. Nanocapsules were then formed through encapsulation of the hydrocarbon by the newly produced polymers at the interfaces of the droplets. The crosslinked structure gradually grew to stabilize the shell morphology. The incorporation of NIPAM into the shell copolymers has been verified by FTIR and solid‐state 13C NMR data. The fact that the number of nanocapsules increases with increasing amounts of DVB and NIPAM supports the formation of nanocapsules following interfacial (co)polymerization. Therefore, a mechanism for the formation of nanocapsules through interfacial (co)polymerization induced by NIPAM and DVB is proposed. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1522–1534, 2009
Relationship of psychological characteristics and self‐efficacy in gastrointestinal cancer survivors
Authors: Kohno Yuuta , Maruyama Michio , Matsuoka Yutaka , Matsushita Toshiko , Koeda Michihiko , Matsushima Eisuke
Published: February 2009

To characterize gastrointestinal cancer survivors' ability to psychologically adjust, we examined the relationship between psychological characteristics (quality of life (QOL), anxiety, depression, and post‐traumatic stress symptoms) and self‐efficacy (perceived ability to initiate coping strategies). Forty‐seven subjects (32 males and 15 females) were recruited from outpatient clinics or general surgical wards after readmission for therapy unrelated to cancer. All had undergone treatment for gastrointestinal cancer. Japanese version of the Functional Assessment of Cancer Therapy—General (FACT‐G), Japanese version of Hospital Anxiety and Depression Scale (HADS), Japanese version of Impact of Event Scale—Revised (IES‐R), and The Self‐Efficacy Scale for Advanced Cancer (SEAC) were administered. Correlation analyses revealed a statistically significant positive correlation between three subscales of SEAC and QOL (total of FACT‐G value) and a significant negative correlation between anxiety, depression (the total of HADS value), post‐traumatic stress symptoms (the total of IES‐R value), and SEAC. In multiple regression analysis, the influence from Affect Regulation Efficacy (subscale of SEAC) was the largest in anxiety and post‐traumatic stress symptoms while the influence from Activities of Daily Living Efficacy (subscale of SEAC) was the largest in QOL and depression. Our findings revealed that a strong relationship between self‐efficacy and psychological adjustment, and that there should be several psychological intervention forms performed at various treatment stages to enhance self‐efficacy in this population of gastrointestinal cancer survivors. These results also imply the effectiveness of interventions on self‐efficacy for gastrointestinal cancer survivors and the influence of psychological factors such as QOL, anxiety, depression, and post‐traumatic stress symptoms. Copyright © 2009 John Wiley & Sons, Ltd.
Waist circumference associated with pulmonary function in children
Authors: Chen Yue , Rennie Donna , Cormier Yvon , Dosman James A.
Published: February 2009

In adults abdominal obesity is related to lung dysfunction and waist circumference (WC) predicts pulmonary function. It is not known how WC affects pulmonary function in children. A cross‐sectional study of 718 children 6–17 years of age was conducted in a rural community to determine the predictability of WC for pulmonary function in children. Height, weight, WC, and pulmonary function were measured. Multivariate analysis was conducted. WC was positively associated with FVC and FEV1 and was more strongly associated with FVC than with FEV1. Increase in WC significantly predicted a reduction in FEV1/FVC. After adjustment for sex, age, and height, an increase of 1 cm for WC was associated with an increase of 7 ml of FVC and 4 ml of FEV1, and with an increase of 4 ml of FVC and 2 ml of FEV1 with an additional adjustment for weight. Height and weight were not significantly associated with FEV1/FVC. WC but not body mass index predicted a decline of FEV1/FVC. WC had a larger impact on FVC than FEV1. WC, but not BMI, was negatively associated with FEV1/FVC in children. Pediatr Pulmonol. 2009; 44:216–221. © 2009 Wiley‐Liss, Inc.
Severity of childhood community‐acquired pneumonia and chest radiographic findings
Authors: Kin Key Ng , Araújo‐Neto César Augusto , Nascimento‐Carvalho Cristiana Maria
Published: February 2009

To assess if chest radiographic findings present on admission are associated with severity of childhood community‐acquired pneumonia (CAP), a total of 161 children hospitalized with pulmonary infiltrate were enrolled in the study; 48 (30%) patients were excluded because of presence of bilateral chest radiographic alterations (33; 20%) and presence of underlying diseases (15; 9%). According to WHO and BTS criteria, severe CAP was present in 57 (50%) and in 96 (85%) cases, respectively; 29 (26%) were aged less than 1 year. The median age (months) was 22 (mean 24 ± 14, range 2–58). Overall, radiographic finding was right‐sided in 77 (68%) cases and the upper lobe was compromised in 36 (32%) cases. By analyzing data stratified to age, the frequency of upper lobe involvement was significantly higher among severe cases (WHO criteria) only for those patients aged ≥1 year (13/35 [37%] vs. 7/45 [16%], P = 0.03, OR [95% CI] 3.2 [1.1–9.2]). The specificity and positive predictive value of upper lobe involvement for severity among the latter group of patients were 84% (95% CI 70–93%) and 65% (95% CI 41–84%), respectively. No association was found by using the BTS criteria. The admission chest radiography was useful to predict severity of children aged ≥1 year hospitalized with CAP. Pediatr Pulmonol. 2009; 44:249–252. © 2009 Wiley‐Liss, Inc.
Tricuspid regurgitant jet velocity elevation and its relationship to lung function in pediatric sickle cell disease
Authors: Liem Robert I. , Nevin Mary A. , Prestridge Adrienne , Young Luciana T. , Thompson Alexis A.
Published: February 2009

Concerns about the morbidity and mortality associated with tricuspid regurgitant jet velocity (TRJV) elevation, which may indicate pulmonary hypertension (PHT), in adults with sickle cell disease (SCD) have prompted growing interest in screening the pediatric sickle cell population. The goals of our study were to estimate the prevalence of TRJV elevation and determine its relationship to pulmonary function in children and young adults with SCD at baseline. Seventy‐eight subjects (10–24 years old) with SCD underwent prospective screening by Doppler echocardiogram (ECHO), complete lung function evaluation, and laboratory testing as part of standard care at steady state. Tricuspid regurgitation was quantifiable in 68/78 (87%) subjects and peak TRJV was ≥2.5 m/sec in 26/78 (33.3%) evaluated. The frequency of obstruction, restriction, or abnormal gas exchange found on lung function evaluation was not significantly different in subjects with and without TRJV elevation. However, significant inverse correlations were observed between TRJV and both % predicted forced vital capacity (FVC) (r = −0.29, P = 0.022) and oxygen saturation (r = −0.26, P = 0.036). When compared to subjects without TRJV elevation, subjects with TRJV elevation had significantly lower % predicted forced expiratory volume in 1 sec (FEV1) (78.9 ± 14.4 vs. 86.6 ± 13.0%, P = 0.023), FVC (82.8 ± 14.1 vs. 90.7 ± 12.9%, P = 0.017), and oxygen saturation (95.8 ± 3.2 vs. 97.5 ± 2.4%, P = 0.016). We found that the combination of low hemoglobin and low % predicted FVC best predicted TRJV elevation (χ2 = 17.05, P = 0.001) in our cohort, correctly identifying 70% of cases and resulting in positive and negative predictive values of 60 and 74%, respectively. We conclude that in this young population with SCD, TRJV elevation that is not significantly associated with abnormal lung function is common at baseline. Pediatr Pulmonol. 2009; 44:281–289. © 2009 Wiley‐Liss, Inc.
Solution structure of the RNA binding domain in the human muscleblind‐like protein 2
Authors: He Fahu , Dang Weirong , Abe Chikage , Tsuda Kengo , Inoue Makoto , Watanabe Satoru , Kobayashi Naohiro , Kigawa Takanori , Matsuda Takayoshi , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Harada Takushi , Tomabechi Yuri , Terada Takaho , Shirouzu Mikako , Tanaka Akiko , Güntert Peter , Muto Yutaka , Yokoyama Shigeyuki
Published: February 2009

The muscleblind‐like (MBNL) proteins 1, 2, and 3, which contain four CCCH zinc finger motifs (ZF1–4), are involved in the differentiation of muscle inclusion by controlling the splicing patterns of several pre‐mRNAs. Especially, MBNL1 plays a crucial role in myotonic dystrophy. The CCCH zinc finger is a sequence motif found in many RNA binding proteins and is suggested to play an important role in the recognition of RNA molecules. Here, we solved the solution structures of both tandem zinc finger (TZF) motifs, TZF12 (comprising ZF1 and ZF2) and TZF34 (ZF3 and ZF4), in MBNL2 from Homo sapiens. In TZF12 of MBNL2, ZF1 and ZF2 adopt a similar fold, as reported previously for the CCCH‐type zinc fingers in the TIS11d protein. The linker between ZF1 and ZF2 in MBNL2 forms an antiparallel β‐sheet with the N‐terminal extension of ZF1. Furthermore, ZF1 and ZF2 in MBNL2 interact with each other through hydrophobic interactions. Consequently, TZF12 forms a single, compact global fold, where ZF1 and ZF2 are approximately symmetrical about the C2 axis. The structure of the second tandem zinc finger (TZF34) in MBNL2 is similar to that of TZF12. This novel three‐dimensional structure of the TZF domains in MBNL2 provides a basis for functional studies of the CCCH‐type zinc finger motifs in the MBNL protein family.
A summary of the measured pK values of the ionizable groups in folded proteins
Authors: Grimsley Gerald R. , Scholtz J. Martin , Pace C. Nick
Published: February 2009

We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 ± 1.2 (139); Glu 4.2 ± 0.9 (153); His 6.6 ± 1.0 (131); Cys 6.8 ± 2.7 (25); Tyr 10.3 ± 1.2 (20); Lys 10.5 ± 1.1 (35); C‐terminus 3.3 ± 0.8 (22) and N‐terminus 7.7 ± 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold
Authors: Fazelinia Hossein , Cirino Patrick C. , Maranas Costas D.
Published: February 2009

One of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. In this study, we introduce a new computational procedure OptGraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. This is accomplished by introducing a two‐level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the departure from a set of geometric restraints using mixed‐integer linear optimization. On identifying the suitable locations that can accommodate the new binding pocket, CHARMM energy calculations are employed to identify what mutations in the neighboring residues, if any, are needed to ensure that the minimum energy conformation of the binding pocket conserves the desired geometry. This computational framework is benchmarked against the results available in the literature for engineering a copper binding site into thioredoxin protein. Subsequently, OptGraft is used to guide the transfer of a calcium‐binding pocket from thermitase protein (PDB: 1thm) into the first domain of CD2 protein (PDB:1hng). Experimental characterization of three de novo redesigned proteins with grafted calcium‐binding centers demonstrated that they all exhibit high affinities for terbium (Kd ∼ 22, 38, and 55 μM) and can selectively bind calcium over magnesium.
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution‐state structure of the nucleocapsid protein from HIV‐1
Authors: Summers Michael F. , Henderson Louis E. , Chance Mark R. , South Terri L. , Blake Paul R. , Perez‐Alvarado Gabriela , Bess Julian W. , Sowder Raymond C. , Arthur Larry O. , Sagi Irit , Hare Dennis R.
Published: February 2009

All retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys‐1His array (CCHC = C‐X2‐C‐X4‐H‐X4‐C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc‐binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc‐edge extended X‐ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus‐bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840–847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys‐1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV‐1 NC protein and have determined its three‐dimensional solution‐state structure. The CCHC arrays of HIV‐1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV‐1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid‐binding results provide a basis for the rational design of new NC‐targeted antiviral agents and vaccines for the control of AIDS.
Identification of the posttranslational modifications of bovine lens αB‐crystallins by mass spectrometry
Authors: Smith Jean B. , Sun Yiping , Smith David L. , Green Brian
Published: February 2009

A combination of mass spectrometric techniques has been used to investigate the amino acid sequence and post‐translational modifications of αB‐crystallin isolated from bovine lenses by gel filtration chromatography and reversed‐phase high performance liquid chromatography. Chromatographic fractions were analyzed by electrospray ionization mass spectrometry to determine the homogeneity and molecular weights of proteins in the fractions. The αB‐crystallin primary gene product, its mono‐ and diphosphorylated forms, its N‐ and C‐terminal truncated forms, as well as other lens proteins unrelated to the αB‐crystallins were identified by their molecular weights. Detailed information about the sites of phosphorylation, as well as evidence supporting reassignment of Asn to Asp at position 80, was obtained by analyzing proteolytic digests of these proteins by fast atom bombardment mass spectrometry. Results of this investigation indicate that αB‐crystallin is phosphorylated in vivo at Ser 45, Ser 59, and either Ser 19 or 21. From the specificity of phosphorylation of α‐crystallins, it appears that there may be two different kinases responsible for their phosphorylation.
Protein classification artificial neural system
Authors: Wu Cathy , Whitson George , Mclarty Jerry , Ermongkonchai Adisorn , Chang Tzu‐Chung
Published: February 2009

A neural network classification method is developed as an alternative approach to the large database search/organization problem. The system, termed Protein Classification Artificial Neural System (ProCANS), has been implemented on a Cray supercomputer for rapid superfamily classification of unknown proteins based on the information content of the neural interconnections. The system employs ann‐gram hashing function that is similar to thek‐tuple method for sequence encoding. A collection of modular back‐propagation networks is used to store the large amount of sequence patterns. The system has been trained and tested with the first 2,148 of the 8,309 entries of the annotated Protein Identification Resource protein sequence database (release 29). The entries included the electron transfer proteins and the six enzyme groups (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases), with a total of 620 superfamilies. After a total training time of seven Cray central processing unit (CPU) hours, the system has reached a predictive accuracy of 90%. The classification is fast (i.e., 0.1 Cray CPU second per sequence), as it only involves a forward‐feeding through the networks. The classification time on a full‐scale system embedded with all known superfamilies is estimated to be within 1 CPU second. Although the training time will grow linearly with the number of entries, the classification time is expected to remain low even if there is a 10–100‐fold increase of sequence entries. The neural database, which consists of a set of weight matrices of the networks, together with the ProCANS software, can be ported to other computers and made available to the genome community. The rapid and accurate superfamily classification would be valuable to the organization of protein sequence databases and to the gene recognition in large sequencing projects.
Cysteinyl peptides labeled by dibromobutanedione in reaction with rabbit muscle pyruvate kinase
Authors: Vollmer Sara H. , Colman Roberta F.
Published: February 2009

The bifunctional reagent 1,4‐dibromobutanedione (DBBD) reacts covalently with pyruvate kinase from rabbit muscle to cause inactivation of the enzyme at a rate that is linearly dependent on the reagent concentration, giving a second order rate constant of 444 min−1 M−1. The individual substrates phosphoenolpyruvate (with KCl), ADP, or ATP in the presence of divalent metal cation provide marked protection against inactivation suggesting that reaction occurs in the region of the active site. The limited incorporation of DBBD into pyruvate kinase was measured by reduction of the carbonyl groups of the enzyme‐bound reagent using [3H]NaBH4. When pyruvate kinase was reacted with 120 μM DBBD at pH 7.0 for 50 min in the absence of protectants, 1.8 mol of tritium/mol of subunit was incorporated, whereas in the presence of phosphoenolpyruvate with KCl, only 1.0 mol of tritium was incorporated per mole of subunit.

Modified peptides were isolated from tryptic digests of pyruvate kinase. Reaction of enzyme in the presence of substrate (showing no activity loss) yielded a single peptide, Asn‐Ile‐X1‐Lys, where X1 corresponds to Cys164 of the known amino acid sequence of muscle pyruvate kinase. In the absence of protectants, reaction for 10 min (when the enzyme retained substantial activity) yielded Asn‐Ile‐X1‐Lys as the major labeled peptide, whereas reaction for 50 min (when the enzyme was 88% inactivated) yielded predominantly Asn‐Ile‐X1‐Lys cross‐linked to X2‐Asp‐Glu‐Asn‐Ile‐Leu‐Trp‐Leu‐Asp‐Tyr‐Lys, where X2 corresponds to Cys151. Because activity loss correlates with the appearance of the cross‐linked peptides but not with formation of Asn‐Ile‐X1‐Lys, inactivation is likely caused by the reaction leading to the cross‐link between Cys151 and Cys164. The distance between the α‐carbons of these residues in the crystal structure is 15.5 Å, whereas only 12.0 Å can be spanned by the two side chains linked by a dioxobutyl group, suggesting either that pyruvate kinase undergoes a conformational change in forming the cross‐link or that local rapid fluctuations in structure occur in solution to the extent of 3.5 Å in this region of pyruvate kinase.
A protease‐sensitive site in the proposed Ca2+‐binding region of human serum amyloid P component and other pentraxins
Authors: Kinoshita Carol M. , Gewurz Anita T. , Siegel Joan N. , Ying Shan‐Ching , Gupta Rajesh K. , Huckman Robert , Gewurz Henry , Hugli Tony E. , Coe John E.
Published: February 2009

Serum amyloid P component (SAP) is a decamer of 10 identical 25.5‐kDa subunits. Limited proteolysis of SAP with α‐chymotrypsin cleaves the subunit into two fragments of 18 and 7.5 kDa, although the fragments stay together in the decamer under nondenaturing conditions. Proteolysis does not occur in the presence of Ca2+ (10 mM). Cleavage with α‐chymotrypsin prevents the Ca2+‐dependent binding of SAP to zymosan extract, nucleosomes, and DNA. The α‐chymotrypsin cleavage site identified is in a region of SAP that is highly conserved in members of the human C‐reactive protein (CRP) family of proteins (pentraxins) to which SAP belongs and is similar to the Ca2+‐binding site in calmodulin and related Ca2+‐binding proteins (Nguyen, N.Y., Suzuki, A., Boykins, R.A., & Liu, T.‐Y., 1986, J. Biol. Chem. 261, 10456–10465). Treatment of SAP with other proteases (trypsin, Pronase, and Nagarse protease) yields fragmentation patterns upon sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) that are similar to those obtained with α‐chymotrypsin. Two other members of the pentraxin family of proteins, hamster female protein and rabbit CRP, also exhibit similar fragmentation patterns on SDS‐PAGE when treated with the various proteases. Recently, it has been shown that the homologous protein, human CRP, is cleaved in the same homologous position as cleavage of SAP by α‐chymotrypsin, resulting in the loss of Ca2+ binding (as shown by equilibrium dialysis) and Ca2+‐dependent binding reactivities (Kinoshita, C.M., Ying, S.‐C., Hugli, T.E., Siegel, J.N., Potempa, L.A., Jiang, H.J., Houghten, R.A., & Gewurz, H., 1989, Biochemistry 28, 9840–9848). These results indicate that the protease sensitivity of this proposed Ca2+‐binding region has been conserved and may play an important regulatory role, perhaps via the control of Ca2+‐dependent properties of these proteins.
Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli
Authors: Mauzy C.A. , Hermodson M.A.
Published: February 2009

The DNA sequence encoding the rbs repressor protein, RbsR, has been determined. Amino acid sequence analyses of the product of an rbsR‐lacZ fusion and of affinity‐purified RbsR demonstrate that translation begins at an unusual codon, TTG, and that the initial amino acid is removed during maturation of the protein. DNA‐binding assays indicate that RbsR binds to a region of perfect dyad symmetry spanning the rbs operon transcriptional start site and that the affinity for the rbs operator is reduced by addition of ribose, consistent with ribose being the inducer of the operon. RbsR is a member of a family of homologous repressor proteins having very similar DNA‐binding sites and binding to similar operator sequences. [RbsR PIR accession number A41828.]
Cis proline mutants of ribonuclease A. II. Elimination of the slow‐folding forms by mutation
Authors: Schultz David A. , Baldwin Robert L. , Schmid Franz X.
Published: February 2009

Ribonuclease A is known to form an equilibrium mixture of fast‐folding (UF) and slow‐folding (US) species. Rapid unfolding to UF is then followed by a reaction in the unfolded state, which produces a mixture of UF, USII, USI, and possibly also minor populations of other US species. The two cis proline residues, P93 and P114, are logical candidates for producing the major US species after unfolding, by slow cis → trans isomerization. Much work has been done in the past on testing this proposal, but the results have been controversial. Site‐directed mutagenesis is used here. Four single mutants, P93A, P93S, P114A, and P114G, and also the double mutant P93A, P114G have been made and tested for the formation of US species after unfolding. The single mutants P114G and P114A still show slow isomerization reactions after unfolding that produce US species; thus, Pro 114 is not required for the formation of at least one of the major US species of ribonuclease A. Both the refolding kinetics and the isomerization kinetics after unfolding of the Pro 93 single mutants are unexpectedly complex, possibly because the substituted amino acid forms a cis peptide bond, which should undergo cis → trans isomerization after unfolding. The kinetics of peptide bond isomerization are not understood at present and the Pro 93 single mutants cannot be used yet to investigate the role of Pro 93 in forming the US species of ribonuclease A.

The double mutant P93A, P114G shows single exponential kinetics measured by CD, and it shows no evidence of isomerization after unfolding. Thus, the unfolding and refolding kinetics of the double mutant indicate that replacement of Pro 93 and Pro 114 has removed the residues responsible for forming the major US species. This result, taken together with data for the Pro 114 single mutants, indicates that Pro 93 and Pro 114 are collectively responsible for forming the major US species.
Inhibitory effects of HSP70 chaperones on nascent polypeptides
Authors: Ryan Christine , Schlesinger Milton J. , Stevens Tom H.
Published: February 2009

Several of the major heat shock proteins (HSPs) function normally as molecular chaperones to prevent aggregation of immature polypeptides and thereby facilitate folding and oligomerization. To determine their effect on nascent polypeptides, we added purified preparations of different isoforms of HSP70 to in vitro translation reactions primed by the 26S mRNA of Sindbis virus, which encodes an autoprotease that functions cotranslationally, or by the mRNA encoding the yeast vacuolar H+ATPase, which is formed by a novel transpeptidase activity that removes the central region of the initial polypeptide. In the presence of HSP70s both the autoprotease and transpeptidase activities were inhibited, indicating that these chaperones can interact with nascent polypeptides and, in the cases studied here, perturb their normal structures.
Multiple phosphate positions in the catalytic site of glycogen phosphorylase: Structure of the pyridoxal‐5′‐pyrophosphate coenzyme‐substrate analog
Authors: Sprang Stephen R. , Madsen Neil B. , Withers Stephen G.
Published: February 2009

The three‐dimensional structure of an R‐state conformer of glycogen phosphorylase containing the coenzyme‐substrate analog pyridoxal‐5′‐diphosphate at the catalytic site (PLPP‐GPb) has been refined by X‐ray crystallography to a resolution of 2.87 Å. The molecule comprises four subunits of phosphorylase related by approximate 222 symmetry. Whereas the quaternary structure of R‐state PLPP‐GPb is similar to that of phosphorylase crystallized in the presence of ammonium sulfate (Barford, D. & Johnson, L.N., 1989, Nature 340, 609–616), the tertiary structures differ in that the two domains of the PLPP‐GPb subunits are rotated apart by 5° relative to the T‐state conformation. Global differences among the four subunits suggest that the major domains of the phosphorylase subunit are connected by a flexible hinge. The two different positions observed for the terminal phosphate of the PLPP are interpreted as distinct phosphate subsites that may be occupied at different points along the reaction pathway. The structural basis for the unique ability of R‐state dimers to form tetramers results from the orientation of subunits with respect to the dyad axis of the dimer. Residues in opposing dimers are in proper registration to form tetramers only in the R‐state.
Avian 3‐hydroxy‐3‐methylglutaryl‐CoA lyase: Sensitivity of enzyme activity to thiol/disulfide exchange and identification of proximal reactive cysteines
Authors: Hruz Paul W. , Miziorko Henry M.
Published: February 2009

Catalysis by purified avian 3‐hydroxy‐3‐methylglutaryl‐CoA lyase is critically dependent on the reduction state of the enzyme, with less than 1% of optimal activity being observed with the air‐oxidized enzyme. The enzyme is irreversibly inactivated by sulfhydryl‐directed reagents with the rate of this inactivation being highly dependent upon the redox state of a critical cysteine. Methylation of reduced avian lyase with 1 mM 4‐methylnitrobenzene sulfonate results in rapid inactivation of the enzyme with a kinact of 0.178 min−1. The oxidized enzyme is inactivated at a sixfold slower rate (kinact = 0.028 min−1). Inactivation of the enzyme with the reactive substrate analog 2‐butynoyl‐CoA shows a similar dependence upon the enzyme's redox state, with a sevenfold difference in kinact observed with oxidized vs. reduced forms of the enzyme. Chemical cross‐linking of the reduced enzyme with stoichiometric amounts of the bifunctional reagents 1,3‐dibromo‐2‐propanone (DBP) or N, N′‐ortho‐phenylenedimaleimide (PDM) coincides with rapid inactivation. Sodium dodecyl sulfate‐polyacrylamide gel electrophoresis of enzyme treated with bifunctional reagent reveals a band of twice the molecular weight of the lyase monomer, indicating that an intersubunit cross‐link has been formed. Differential labeling of native and cross‐linked protein with [1‐14C]iodoacetate has identified as the primary cross‐linking target a cysteine within the sequence VSQAACR, which maps at the carboxy‐terminus of the cDNA‐deduced sequence of the avian enzyme (Mitchell, G.A., et al., 1991, Am. J. Hum. Genet. 49, 101). In contrast, bacterial HMG‐CoA lyase, which contains no corresponding cysteine, is not cross‐linked by comparable treatment with bifunctional reagent. These results provide evidence for a potential regulatory mechanism for the eukaryotic enzyme via thiol/disulfide exchange and identify a cysteinyl residue with the reactivity and juxtaposition required for participation in disulfide formation.