bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pressure‐induced changes in the solution structure of the GB1 domain of protein G
Authors: Wilton David J. , Tunnicliffe Richard B. , Kamatari Yuji O. , Akasaka Kazuyuki , Williamson Mike P. 
Published: December 2007

AbstractThe solution structure of the GB1 domain of protein G at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy‐minimised low‐pressure structure using 1H chemical shifts. Two separate changes can be characterised: a compression/distortion, which is linear with pressure; and a stabilisation of an alternative folded state. On application of pressure, linear chemical shift changes reveal that the backbone structure changes by about 0.2 Å root mean square, and is compressed by about 1% overall. The α‐helix compresses, particularly at the C‐terminal end, and moves toward the β‐sheet, while the β‐sheet is twisted, with the corners closest to the α‐helix curling up towards it. The largest changes in structure are along the second β‐strand, which becomes more twisted. This strand is where the protein binds to IgG. Curved chemical shift changes with pressure indicate that high pressure also populates an alternative structure with a distortion towards the C‐terminal end of the helix, which is likely to be caused by insertion of a water molecule. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin
Authors: Xie Bin‐Bin , Chen Xiu‐Lan , Zhang Xi‐Ying , He Hai‐Lun , Zhang Yu‐Zhong , Zhou Bai‐Cheng 
Published: December 2007

AbstractIdentification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41–0.71 for eight intraprotein interaction examples, and 0.07–0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three‐dimensional protein structure data are available. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Complex assembly mechanism and an RNA‐binding mode of the human p14‐SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses
Authors: Kuwasako Kanako , Dohmae Naoshi , Inoue Mio , Shirouzu Mikako , Taguchi Seiichi , Güntert Peter , Séraphin Bertrand , Muto Yutaka , Yokoyama Shigeyuki 
Published: December 2007

AbstractThe spliceosomal protein p14, a component of the SF3b complex in the U2 small nuclear ribonucleoprotein (snRNP), is essential for the U2 snRNP to recognize the branch site adenosine. The elucidation of the dynamic process of the splicing machinery rearrangement awaited the solution structural information. We identified a suitable complex of human p14 and the SF3b155 fragment for the determination of its solution structure by NMR. In addition to the overall structure of the complex, which was recently reported in a crystallographic study (typical RNA recognition motif fold β1‐α1‐β2‐β3‐α2‐β4 of p14, and αA‐βA fold of the SF3b155 fragment), we identified three important features revealed by the NMR solution structure. First, the C‐terminal extension and the nuclear localization signal of p14 (α3 and α4 in the crystal structure, respectively) were dispensable for the complex formation. Second, the proline‐rich segment of SF3b155, following βA, closely approaches p14. Third, interestingly, the β1‐α1 loop and the α2‐β4 β‐hairpin form a positively charged groove. Extensive mutagenesis analyses revealed the functional relevance of the residues involved in the protein–protein interactions: two aromatic residues of SF3b155 (Phe408 and Tyr412) play crucial roles in the complex formation, and two hydrophobic residues (Val414 and Leu415) in SF3b 155 serve as an anchor for the complex formation, by cooperating with the aromatic residues. These findings clearly led to the conclusion that SFb155 binds to p14 with three contact points, involving Phe408, Tyr412, and Val414/Leu415. Furthermore, to dissect the interactions between p14 and the branch site RNA, we performed chemical‐shift‐perturbation experiments, not only for the main‐chain but also for the side‐chain resonances, for several p14‐SF3b155 complex constructs upon binding to RNA. These analyses identified a positively charged groove and the C‐terminal extension of p14 as RNA‐binding sites. Strikingly, an aromatic residue in the β1‐α1 loop, Tyr28, and a positively charged residue in the α2‐β4 β‐hairpin, Agr85, are critical for the RNA‐binding activity of the positively charged groove. The Tyr28Ala and Arg85Ala point mutants and a deletion mutant of the C‐terminal extension clearly revealed that their RNA binding activities were independent of each other. Collectively, this study provides details for the protein‐recognition mode of p14 and insight into the branch site recognition. Proteins 2008. © 2007 Wiley‐Liss, Inc.
In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin
Authors: Cherezov Vadim , Liu Wei , Derrick Jeremy P. , Luan Binquan , Aksimentiev Aleksei , Katritch Vsevolod , Caffrey Martin 
Published: December 2007

AbstractOpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)‐containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10‐stranded β‐barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the β‐barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius
Authors: Mandrich Luigi , Menchise Valeria , Alterio Vincenzo , De Simone Giuseppina , Pedone Carlo , Rossi Mosè , Manco Giuseppe 
Published: December 2007

AbstractRecent mutagenic and molecular modelling studies suggested a role for glycine 84 in the putative oxyanion loop of the carboxylesterase EST2 from Alicyclobacillus acidocaldarius. A 114 times decrease of the esterase catalytic activity of the G84S mutant was observed, without changes in the thermal stability. The recently solved three‐dimensional (3D) structure of EST2 in complex with a HEPES molecule permitted to demonstrate that G84 (together with G83 and A156) is involved in the stabilization of the oxyanion through a hydrogen bond from its main chain NH group. The structural data in this case did not allowed us to rationalize the effect of the mutation, since this hydrogen bond was predicted to be unaltered in the mutant. Since the mutation could shed light on the role of the oxyanion loop in the HSL family, experiments to elucidate at the mechanistic level the reasons of the observed drop in k cat were devised. In this work, the kinetic and structural features of the G84S mutant were investigated in more detail. The optimal temperature and pH for the activity of the mutated enzyme were found significantly changed (T = 65°C and pH = 5.75). The catalytic constants K M and Vmax were found considerably altered in the mutant, with ninefold increased K M and 14‐fold decreased Vmax, at pH 5.75. At pH 7.1, the decrease in k cat was much more dramatic. The measurement of kinetic constants for some steps of the reaction mechanism and the resolution of the mutant 3D structure provided evidences that the observed effects were partly due to the steric hindrance of the S84‐OH group towards the ester substrate and partly to its interference with the nucleophilic attack of a water molecule on the second tetrahedral intermediate. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Numerical nonlinear observers using pseudo‐Newton‐type solvers
Authors: Hanba Shigeru 
Published: December 2007

AbstractIn constructing a globally convergent numerical nonlinear observer of Newton‐type for a continuous‐time nonlinear system, a globally convergent nonlinear equation solver with a guaranteed rate of convergence is necessary. In particular, the solver should be Jacobian free, because an analytic form of the state transition map of the nonlinear system is generally unavailable. In this paper, two Jacobian‐free nonlinear equation solvers of pseudo‐Newton type that fulfill these requirements are proposed. One of them is based on the finite difference approximation of the Jacobian with variable step size together with the line search. The other uses a similar idea, but the estimate of the Jacobian is mostly updated through a BFGS‐type law. Then, by using these solvers, globally stable numerical nonlinear observers are constructed. Numerical results are included to illustrate the effectiveness of the proposed methods. Copyright © 2007 John Wiley & Sons, Ltd.
Tensile Tests of Polymers at Low Temperatures in the Environmental Scanning Electron Microscope: An Improved Cooling Platform
Authors: Zankel A. , Poelt P. , Gahleitner M. , Ingolic E. , Grein C. 
Published: December 2007

AbstractThe investigation of the fracture behavior of polymers in the environmental scanning electron microscope (ESEM) can provide information about the correlation between the microstructure of a specimen and the macroscopic stress–strain characteristic. As the mechanical properties of polymers change dramatically at the glass transition temperature, cooling of the specimens during the tensile tests can yield very valuable information about the influence of individual components of polymer blends on the fracture behavior of the material. A serious problem in this connection is the poor heat conductivity of polymers. A commercially available cooling platform, which can be mounted on the tensile stage used for the tests was substantially modified to both enhance the heat transfer between platform and specimen, and to minimize the temperature gradient along the specimen.The first experiments on modified polypropylene specimens already delivered some unexpected results. Fibril‐like structures appeared at the crack tip that would not be expected at temperatures below the glass transition temperature of the polymer blend. SCANNING 29: 261–269, 2007. © 2007 Wiley Periodicals, Inc.
Effect of Surface Conjugation Chemistry on the Sensitivity of Microcantilever Sensors
Authors: Kim Dae Jung , Weeks Brandon L. , Hope‐Weeks Louisa J. 
Published: December 2007

AbstractMicrocantilever sensors are an offshoot of atomic force microscopy and are useful tools for effectively detecting a target biomolecule. The recognition of the target molecule on the biosensor is based on the physical bending of the microcantilever, which is driven by a specific molecular interaction between the target molecule and the sensor surface. In this study, to enhance the sensitivity of the microcantilever sensor, the sensor surface was modified through a surface conjugation method using self‐assembled monolayers (SAMs) and heterobifunctional cross‐linkers. After the surface modification of the microcantilever sensor, the sensitivity for L‐cysteine was recorded. The detection of L‐cysteine was influenced by the active site and the molecular size of the cross‐linked compound attached onto the surface of the microcantilever. SCANNING 29: 245–248, 2007. © 2007 Wiley Periodicals, Inc.
The Sikh spiritual model of counseling
Authors: Singh Kala 
Published: December 2007

AbstractIn accordance with the holistic principles of modern medicine, this paper will present the Sikh religious and spiritual view of mental health. With the continuing migration of a large number of South Asians, especially the Sikhs, to Western countries, mental health professionals should be aware of their clients' world‐view and cultural/religious specific models of counseling. Use of Sikh spirituality can reduce stress; help in treating psychosomatic disorders; and improve mental health of the individual and of the community. This paper will conclude that as the Sikh religion is a universal religion, everyone can use Sikh spirituality. Copyright © 2007 John Wiley & Sons, Ltd.
Early childhood teachers' views of nature of science: The influence of intellectual levels, cultural values, and explicit reflective teaching
Authors: Akerson Valarie L. , Buzzelli Cary A. , Donnelly Lisa A. 
Published: December 2007

AbstractThis study tracked the influence of explicit reflective instructional methods on cultural values, ethical and intellectual development, and the relationship of these with preservice teachers' views of nature of science (NOS). The researchers used the Views of Nature of Science Form B (VNOS B) to describe NOS views, the Learning Context Questionnaire (LCQ) to classify preservice teachers' ethical and intellectual positions using Perry's scheme, and the Schwartz Values Inventory (SVI) to measure preservice teachers' cultural values. The interventions took place in two concurrent courses: a science methods course, and a foundations of early childhood course. The science methods course explicitly emphasized NOS throughout the semester, and the foundations of early childhood course reinforced these ideas through cultural activities that stressed empirical evidence. Analysis of data showed relationships between preservice teachers' Perry positions and responses on the VNOS B with those at higher positions exhibiting more informed NOS views. Relationships between preservice teachers' NOS views and their cultural values were identified, such as those at the dualism position holding achievement more highly for scientists than those at other Perry positions. The values preservice teachers held personally were different from those they held as important for scientists. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 45: 748–770, 2008
Factors influencing elementary and secondary teachers' views on the nature of science
Authors: Morrison Judith A. , Raab Fred , Ingram Dale 
Published: December 2007

AbstractTo explore how elementary teachers may differ from secondary teachers in their views about NOS, a professional development experience involving explicit reflective instruction on NOS, discussions about science with scientists, and exposing the teachers to the practices, techniques, and collaborations fundamental to scientific research was designed. The goal of this professional development project was to immerse the teachers in an environment where science was going on all around them and where they could hear and discuss ideas about NOS, science concepts, and teaching science with scientists and engineers. Data on teachers' views were collected through interviews, questionnaires, reflective papers, and taped class discussions. The findings indicate that secondary teachers with previous experiences in research did not change their views of scientists or NOS; all but one of the elementary and middle school teachers improved in these areas. The factors most influential in affecting teachers' views were the one‐on‐one interviews teachers held with scientists, job shadowing experiences, and explicit, reflective instruction presented on the NOS. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 46: 384–403, 2009
The use of photographs to portray urban ecosystems in six introductory environmental science textbooks
Authors: Sullivan John P. 
Published: December 2007

AbstractThis study examined how photographs in six introductory environmental science texts portrayed the urban environments in which most U.S. students lived. All photographs from all texts were coded to determine whether they depicted urban areas. The urban photographs were then coded to determine what they communicated about the urban environment. The analysis suggested that the texts in this study, though varied in their portrayal of urban ecosystems, did address many of the environmental issues that affected the city. However, urban examples were rarely used to illustrate general ecological concepts that applied to all ecosystems (i.e., biodiversity or evolution). The author contended that “sense of place” theories indicated that more photographs should be dedicated to portraying urban environments as functioning ecosystems. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 45: 1003–1020, 2008
Overlay, Borůvka‐based, Ad‐hoc multicast Protocol: description and performance analysis
Authors: Detti Andrea , Blefari‐Melazzi Nicola 
Published: December 2007

AbstractThis paper presents a novel Mobile Ad‐hoc NETworks (MANET) multicast protocol, named Overlay Borůvka‐based Ad‐hoc Multicast Protocol (OBAMP), and evaluates its performance. OBAMP is an overlay protocol: it runs only in the end‐systems belonging to the multicast group. OBAMP has three distinctive features, which give to the protocol a good performance in terms of distribution efficiency: (i) its distribution tree closely resembles the minimum spanning tree; (ii) it exploits broadcast communications; (iii) its design limits not only overlay signaling but also network‐layer signaling. In addition, OBAMP can cope with node failures in a very short time. As a consequence, OBAMP has a low latency and a high delivery ratio, even when the group size increases. To prove these statements, we analyze the performance of OBAMP with ns‐2 and compare it with three state‐of‐the‐art protocols, namely ODMRP (a network‐layer protocol), ALMA, and AMRoute (two overlay protocols). The overlay protocols are assumed to use AODV as underlying routing protocol. Also, we stress that we have implemented OBAMP, in Java, and we have tested it on the field, to prove its feasibility; to allow fellow researchers to reproduce and test our work we published all simulation and implementation codes. Copyright © 2007 John Wiley & Sons, Ltd.
Making the Connections: Community Capacity for Tobacco Control in an Urban African American Community
Authors: Merzel Cheryl , Moon-Howard Joyce , Dickerson Dawn , Ramjohn Destiny , VanDevanter Nancy 
Published: December 2007

AbstractDeveloping community capacity to improve health is a cornerstone of community‐based public health. The concept of community capacity reflects numerous facets and dimensions of community life and can have different meanings in different contexts. This paper explores how members of one community identify and interpret key aspects of their community's capacity to limit the availability and use of tobacco products. Particular attention is given to examining the interrelationship between various dimensions of community capacity in order to better understand the processes by which communities are able to mobilize for social change. The study is based on qualitative analysis of 19 in‐depth interviews with key informants representing a variety of community sectors in Harlem, New York City. Findings indicate that the community is viewed as rich in human and social resources. A strong sense of community identity and connectedness underlies this reserve and serves as a catalyst for action.
Postoperative Fever: To What Is the Body Really Responding?
Authors: Ballestas Helen C. 
Published: December 2007

ABSTRACTTHE PRESENCE OF A POSTOPERATIVE FEVER is not always indicative of an infectious process. Mild temperature elevation may be transient in nature and may arise from the body's response to tissue injury. Fevers that present from two to more than seven days after a surgical procedure may be caused by other physiological responses.PERIOPERATIVE NURSES can target nursing assessments according to the postoperative day on which the fever presents. AORN J 86 (December 2007) 983–988. © AORN, Inc, 2007.
A Team Training Program Using Human Factors to Enhance Patient Safety
Authors: Marshall David A. , Manus Danae A. 
Published: December 2007

ABSTRACTBEGINNING IN 2005, THE AORN FOUNDATION and Safer Healthcare implemented a human factors program based on Crew Resource Management training in five diverse surgical facilities across the United States.HIGHLY INTERACTIVE, CUSTOMIZED training sessions were designed to help clinicians standardize communication, enhance teamwork, implement preprocedure briefings and postprocedure debriefings, maintain situational awareness, and recognize red flags in the workplace. Pretraining and post‐training surveys were used to determine the effectiveness of the program.BRIEF OVERVIEWS from the participating facilities detail specific issues encountered in each setting. AORN J 86 (December 2007) 994‐1011. © AORN, Inc, 2007.
Quantitative studies of ribosome conformational dynamics
Authors: Fraser Christopher S. , Doudna Jennifer A. 
Published: December 2007

AbstractThe ribosome is a dynamic machine that undergoes many conformational rearrangements during the initiation of protein synthesis. Significant differences exist between the process of protein synthesis initiation in eubacteria and eukaryotes. In particular, the initiation of eukaryotic protein synthesis requires roughly an order of magnitude more initiation factors to promote efficient mRNA recruitment and ribosomal recognition of the start codon than are needed for eubacterial initiation. The mechanisms by which these initiation factors promote ribosome conformational changes during stages of initiation have been studied using cross-linking, footprinting, site-directed probing, cryo-electron microscopy, X-ray crystallography, fluorescence spectroscopy and single-molecule techniques. Here, we review how the results of these different approaches have begun to converge to yield a detailed molecular understanding of the dynamic motions that the eukaryotic ribosome cycles through during the initiation of protein synthesis.