bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure is three to ten times more conserved than sequence—A study of structural response in protein cores
Authors: Illergård Kristoffer , Ardell David H. , Elofsson Arne 
Published: April 2009

AbstractProtein structures change during evolution in response to mutations. Here, we analyze the mapping between sequence and structure in a set of structurally aligned protein domains. To avoid artifacts, we restricted our attention only to the core components of these structures. We found that on average, using different measures of structural change, protein cores evolve linearly with evolutionary distance (amino acid substitutions per site). This is true irrespective of which measure of structural change we used, whether RMSD or discrete structural descriptors for secondary structure, accessibility, or contacts. This linear response allows us to quantify the claim that structure is more conserved than sequence. Using structural alphabets of similar cardinality to the sequence alphabet, structural cores evolve three to ten times slower than sequences. Although we observed an average linear response, we found a wide variance. Different domain families varied fivefold in structural response to evolution. An attempt to categorically analyze this variance among subgroups by structural and functional category revealed only one statistically significant trend. This trend can be explained by the fact that beta‐sheets change faster than alpha‐helices, most likely due to that they are shorter and that change occurs at the ends of the secondary structure elements. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Characterization of cancer‐linked BRCA1‐BRCT missense variants and their interaction with phosphoprotein targets
Authors: Drikos Ioannis , Nounesis George , Vorgias Constantinos E. 
Published: April 2009

AbstractThe breast cancer tumor suppressor protein BRCA1 is involved in DNA repair and cell cycle control. Mutations at the two C‐terminal tandem (BRCT) repeats of BRCA1 detected in breast tumor patients were identified either to lower the stability of the BRCT domain and/or to disrupt the interaction of BRCT with phoshpopeptides. The aim of this study was to analyze five BRCT pathogenic mutations for their effect on structural integrity and protein stability. For this purpose, the five cancer‐associated BRCT mutants: V1696L, M1775K, M1783T, V1809F, and P1812A were cloned in suitable prokaryotic protein production vectors, and the recombinant proteins were purified in soluble and stable form for further biophysical studies. The biophysical analysis of the secondary structure and the thermodynamic stability of the wild‐type, wt, and the five mutants of the BRCT domain were performed by Circular Dichroism Spectroscopy (CD) and Differential Scanning Microcalorimetry (DSC), respectively. The binding capacity of the wt and mutant BRCT with (pBACH1/BRIP1) and pCtIP were measured by Isothermal Titration Calorimetry (ITC). The experimental results demonstrated that the five mutations of the BRCT domain: (i) affected the thermal unfolding temperature as well as the unfolding enthalpy of the domain, to a varying degree depending upon the induced destabilization and (ii) altered and/or abolished their affinity to synthetic pBACH1/BRIP1 and pCtIP phosphopeptides by affecting the structural integrity of the BRCT active sites. The presented experimental results are one step towards the elucidation of the effect of various missense mutations on the structure and function of BRCA1‐BRCT. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations
Authors: Barbe Sophie , Lafaquière Vincent , Guieysse David , Monsan Pierre , Remaud‐Siméon Magali , André Isabelle 
Published: April 2009

AbstractThe interfacial activation of many lipases at water/lipid interface is mediated by large conformational changes of a so‐called lid subdomain that covers up the enzyme active site. Here we investigated using molecular dynamic simulations in different explicit solvent environments (water, octane and water/octane interface) the molecular mechanism by which the lid motion of Burkholderia cepacia lipase might operate. Although B. cepacia lipase has so far only been crystallized in open conformation, this study reveals for the first time the major conformational rearrangements that the enzyme undergoes under the influence of the solvent, which either exposes or shields the active site from the substrate. In aqueous media, the lid switches from an open to a closed conformation while the reverse motion occurs in organic environment. In particular, the role of a subdomain facing the lid on B. cepacia lipase conformational rearrangements was investigated using position‐restrained MD simulations. Our conclusions indicate that the sole mobility of α9 helix side‐chains of B. cepacia lipase is required for the full completion of the lid conformational change which is essentially driven by α5 helix movement. The role of selected α5 hydrophobic residues on the lid movement was further examined. In silico mutations of two residues, V138 and F142, were shown to drastically modify the conformational behavior of B. cepacia lipase. Overall, our results provide valuable insight into the role played by the surrounding environment on the lid conformational rearrangement and the activation of B. cepacia lipase. Proteins 2009. © 2009 Wiley‐Liss, Inc.
LOPA misapplied: Common errors can lead to incorrect conclusions
Authors: Study Karen A. , Champion John W. 
Published: April 2009

AbstractLayer of Protection Analysis is a powerful tool for quantitative risk assessments. If applied correctly, it can provide quick and efficient guidance on what additional safeguards are needed, if any, to protect against a given scenario. If misapplied, an overly conservative calculation of risk may result in over‐instrumentation, additional life‐cycle costs, and spurious trips. A nonconservative calculation of risk could result in an under‐protected system and unacceptable risk of an undesired consequence occurring.This article describes several categories of common errors, some overly conservative and some nonconservative. Case studies of actual plant scenarios are used to illustrate. © 2009 American Institute of Chemical Engineers Process Saf Prog 2009
Modulation of protein–ligand interactions by photocleavage of a cyclic peptide using phosphatidylinositol 3‐kinase SH3 domain as model system
Authors: Takahashi Isao , Kuroiwa Shigeki , Lindfors Hanna E. , Ndamba Lionel A. , Hiruma Yoshitaka , Yajima Tatsuo , Okishio Nobuyuki , Ubbink Marcellus , Hirota Shun 
Published: April 2009

AbstractTo photomodulate the interaction of the phosphatidylinositol 3‐kinase SH3 domain with a peptide ligand, a cyclic peptide (cyclic‐1) with a photolabile side chain‐to‐side chain linker was synthesized. The conformation of cyclic‐1 differs from that of the parent linear peptide, but becomes identical by UV‐irradiation. Accordingly, the binding affinity of cyclic‐1 to the SH3 domain increased upon conversion of the cyclic to a linear flexible structure by irradiation (Kd: 3.4 ± 1.7 and 0.9 ± 0.3 mM, respectively). These results confirm the usefulness of a photocleavable peptide for photocontrol of peptide–protein interactions. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Aspartic acid scaffold in bradykinin B1 antagonists
Authors: Huszár József , Timár Zoltán , Bogár Ferenc , Penke Botond , Kiss Róbert , Szalai Krisztina Katalin , Schmidt Éva , Papp Andrea , Keserű György 
Published: April 2009

AbstractSeveral novel bradykinin B1 receptor (B1R) antagonists were synthesized utilizing a new aspartic acid scaffold. This core is derived from the highly potent dihydroquinoxalinone scaffold published recently by researchers at Merck (Haet al. Biochem. Biophys. Res. Commun.2005, 331, 159–166). Despite the considerably limited chemical space of B1 antagonists, the synthesized compounds still showed significant biological activity. None of the four most potent compounds showed significant activity on the bradykinin B2 receptor (B2R), consequently they can be considered as valuable starting points for designing more potent and selective B1 antagonists. Furthermore, the synthesis of these aspartic acid derivatives is much simpler than that of the original Merck compounds suggesting efficient parallel synthesis approaches during their optimization. Docking known and novel B1 antagonists into the refined B1R homology model including the second extracellular loop (EC2) underlined the importance of this loop in ligand binding. Comparative binding mode analysis revealed that our novel compounds bind similar to the dihydroquinoxalinone template. Our results indicate that the rigid core of the dihydroquinoxalinone containing B1 antagonists is not crucial for maintaining B1 activity. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Room‐temperature epitaxial growth of high‐quality m ‐plane InGaN films on ZnO substrates
Authors: Shimomoto Kazuma , Kobayashi Atsushi , Ueno Kohei , Ohta Jitsuo , Oshima Masaharu , Fujioka Hiroshi , Amanai Hidetaka , Nagao Satoru , Horie Hideyoshi 
Published: April 2009

AbstractThe authors have grown high‐quality m ‐plane In0.36Ga0.64N (1$ \bar 1 $00) films on ZnO (1$ \bar 1 $00) substrates at room temperature (RT) by pulsed laser deposition (PLD) and have investigated their structural properties. m ‐plane InGaN films grown on ZnO substrates at RT possess atomically flat surfaces with stepped and terraced structures, indicating that the film growth proceeds in a two‐dimensional mode. X‐ray diffraction measurements have revealed that the m ‐plane InGaN films grow without phase separation reactions at RT. The full‐width at half‐maximum values of the 1$ \bar 1 $00 X‐ray rocking curves of films with X‐ray incident azimuths perpendicular to the c ‐ and a‐axis are 88 arcsec and 78 arcsec, respectively. Reciprocal space‐mapping has revealed that a 50 nm thick m ‐plane In0.36Ga0.64N film grows coherently on the ZnO substrate, which can probably explain the low defect density that is observed in the film. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Will quantum chemistry benefit from quantum computers?
Authors: Kaijser Per 
Published: April 2009

AbstractThis article provides a short review over Quantum Computers and their potential capabilities. It explains and discusses some areas for which they have or might have advantages over conventional computers. Special interest is devoted to their potential in solving scientific problems and in particular what they might do for quantum chemistry. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Composite disturbance‐observer‐based control andH∞control for complex continuous models
Authors: Wei Xinjiang , Guo Lei 
Published: April 2009

AbstractA novel type of control scheme combining the disturbance‐observer‐based control (DOBC) withH∞control is proposed for a class of complex continuous models with disturbances. The disturbances are supposed to include two parts. One part in the input channel is generated by an exogenous system with uncertainty, which can represent the harmonic signals with modeling perturbations. The other part is supposed to have the boundedH2‐norm. Parametric uncertainties exist both in concerned plant and in exogenous subsystem. The disturbance observers based on regional pole placement and D‐stability theory are designed and integrated with conventionalH∞control laws. The new composite DOBC andH∞control scheme is applied to complex continuous models for the case with known and unknown nonlinearity, respectively. Then the first type of disturbances can be estimated and rejected, and the second type can be attenuated; simultaneously, the desired dynamic performances can be guaranteed. Simulations for a flight control system are given to demonstrate the effectiveness of the results and compare the proposed results with the previous schemes. Copyright © 2009 John Wiley & Sons, Ltd.
Tracking control for sampled‐data systems with uncertain time‐varying sampling intervals and delays
Authors: van de Wouw N. , Naghshtabrizi P. , Cloosterman M. B. G. , Hespanha J. P. 
Published: April 2009

AbstractIn this paper, a solution to the approximate tracking problem of sampled‐data systems with uncertain, time‐varying sampling intervals and delays is presented. Such time‐varying sampling intervals and delays can typically occur in the field of networked control systems. The uncertain, time‐varying sampling and network delays cause inexact feedforward, which induces a perturbation on the tracking error dynamics, for which a model is presented in this paper. Sufficient conditions for the input‐to‐state stability (ISS) of the tracking error dynamics with respect to this perturbation are given. Hereto, two analysis approaches are developed: a discrete‐time approach and an approach in terms of delay impulsive differential equations. These ISS results provide bounds on the steady‐state tracking error as a function of the plant properties, the control design and the network properties. Moreover, it is shown that feedforward preview can significantly improve the tracking performance and an online extremum seeking (nonlinear programming) algorithm is proposed to online estimate the optimal preview time. The results are illustrated on a mechanical motion control example showing the effectiveness of the proposed strategy and providing insight into the differences and commonalities between the two analysis approaches. Copyright © 2009 John Wiley & Sons, Ltd.
Processing spectral data
Authors: Görlitz L. , Menze B. H. , Kelm B. M. , Hamprecht F. A. 
Published: April 2009

AbstractSpectral images offer more information on complex probes than either conventional imagery (yielding only one or few measurements per voxel) or conventional spectroscopy (resulting in only one or a few spectra per probe) can. Spectral imaging is thus starting to become ubiquitous in areas ranging from materials science and process control to remote sensing and medicine. However, the information concealed in the massive amount of data generated by spectral imaging is not as easily accessible as in conventional (gray value or color) images and as in conventional spectroscopy, hence calling for new methods to analyze and visualize spectral images.Broadly speaking, analysis methods can be classified in terms of the information used in the training phase, and by the extent to which they use spatial context in the analysis. This article gives a brief overview of ‘unsupervised’ methods that require sample spectral images during the training stage as well as specification of a degree of complexity of the sample, either in terms of number of cluster centers or intrinsic dimensionality of the data [principal component analysis (PCA)]. ‘Supervised’ methods, on the other hand, require a training set in which a class membership, or label, is available for each pixel. Our discussion includes methods that deal well with the high dimensionality and high degree of correlation among individual features, such as partial least squares (PLS) and linear discriminant analysis (LDA).All of the above methods ignore the spatial context when applied to individual spectra. Often, the label map can be assumed to exhibit some spatial coherence, a fact that can help in classifying low quality spectra and that can be exploited using conditional or Markov random fields. The methods are illustrated using examples from automated process control and quantitative medical diagnostics. Copyright © 2009 John Wiley & Sons, Ltd.
Polarization Portraits of Single Multichromophoric Systems: Visualizing Conformation and Energy Transfer
Authors: Mirzov Oleg , Bloem Elin , Hania Peter Ralph , Thomsson Daniel , Lin Hongzhen , Scheblykin Ivan G. 
Published: April 2009

AbstractA novel technique, two‐dimensional (2D) polarization single‐molecule imaging, is presented. It is based on measurements and analysis of fluorescence intensity as a function of excitation and emission polarization angles. The technique allows recording of full information on the steady‐state polarization properties of fluorescent objects. It is particularly suitable for application to single multichromophoric systems (molecules or nanoparticles) with energy transfer (ET) between different chromophores (e.g., single fluorescent π‐conjugated polymer chains). The 2D polarization data simultaneously provide information on the conformation of the system and the efficiency of its internal excitation ET. The technique is used to characterize single chains and different kinds of chain aggregates of different conjugated polymers at different temperatures. The 2D polarization measurements reveal a dramatic difference in ET taking place in these systems. Clear temperature dependence of ET is observed for individual aggregates as well as for their statistical ensembles. Also, a dependence on solvent and aggregate size is shown. Additionally, extensive “traditional one‐dimensional” polarization results on the polarization anisotropy of fluorescence excitation and emission are presented. These results and findings are discussed in relation to internal organization of the nano‐objects under study.
Polyaniline/Pt Hybrid Nanofibers: High‐Efficiency Nanoelectrocatalysts for Electrochemical Devices
Authors: Guo Shaojun , Dong Shaojun , Wang Erkang 
Published: April 2009

AbstractA simple and facile procedure to synthesize a novel hybrid nanoelectrocatalyst based on polyaniline (PANI) nanofiber‐supported supra‐high density Pt nanoparticles (NPs) or Pt/Pd hybrid NPs without prior PANI nanofiber functionalization at room temperature is demonstrated. This represents a new type of 1D hybrid nanoelectrocatalyst with several important benefits. First, the procedure is very simple and can be performed at room temperature using commercially available reagents without the need for templates and surfactants. Second, ultra‐high density small “bare” Pt NPs or Pt/Pd hybrid NPs are grown directly onto the surface of the PANI nanofiber, without using any additional linker. Most importantly, the present PANI nanofiber‐supported supra‐high density Pt NPs or Pt/Pd hybrid NPs can be used as a signal enhancement element for constructing electrochemical devices with high performance.
Biosensing by Densely Packed and Optically Coupled Plasmonic Particle Arrays
Authors: Sannomiya Takumi , Sahoo Pratap K. , Mahcicek Davut I. , Solak Harun H. , Hafner Christian , Grieshaber Dorothee , Vörös Janos 
Published: April 2009

AbstractDensely packed plasmonic particle arrays are investigated for biosensing applications. Such particle arrays exhibit interparticle optical coupling creating a strong field between the particles, which is useful for sensing purposes. The sensor properties, such as bulk sensitivity, layer sensitivity, and the depth of sensitivity are investigated with the aid of a multiple multipole program. Sensitivity to the analyte with low concentration is also examined by a dynamic adsorption processes. The detectable concentration limit of streptavidin within 3000 s in the detection system is expected from the signal‐to‐noise to be less than 150 pM.
Bio/Abiotic Interface Constructed from Nanoscale DNA Dendrimer and Conducting Polymer for Ultrasensitive Biomolecular Diagnosis
Authors: Wei Fang , Liao Wei , Xu Zheng , Yang Yang , Wong David T. , Ho Chih‐Ming 
Published: April 2009

AbstractFor sensors detecting immobilized biomarkers, the interface between the surface and the fluid medium plays an important role in determining the levels of signal and noise in the electrochemical detection process. When protein is directly immobilized on the metal electrode, denaturation of the protein by surface–protein interaction results in low activity and low signal level. A conducting polymer‐based interface can prevent the protein conformation change and alleviate this problem. A DNA dendrimer is introduced into the interfacial film on the sensor surface to further improve the sensor performance. DNA dendrimer is a nanoscale dendrite constructed of short DNA sequences, which can be easily incorporated into the abiotic conducting polymer matrix and is biocompatible with most biological species. In this work, DNA dendrimer and polypyrrole (DDPpy) form the bio/abiotic interface on electrochemical sensors. Detection of two salivary protein markers (IL‐8 and IL‐1β) and one mRNA salivary marker (IL‐8) is used to demonstrate the efficiency of the DDPpy sensor. A limit of detection (LOD) of protein of 100–200 fg mL−1 is achieved, which is three orders of magnitude better than that without the DNA dendrimer interface. An LOD of 10 aM is established for IL‐8 mRNA. The typical sample volume used in the detection is 4 µL, thus the LOD reaches only 25 target molecules (40 yoctomole).
Drug/Dye‐Loaded, Multifunctional Iron Oxide Nanoparticles for Combined Targeted Cancer Therapy and Dual Optical/Magnetic Resonance Imaging
Authors: Santra Santimukul , Kaittanis Charalambos , Grimm Jan , Perez J. Manuel 
Published: April 2009

AbstractA biocompatible, multimodal, and theranostic functional iron oxide nanoparticle is synthesized using a novel water‐based method and exerts excellent properties for targeted cancer therapy, and optical and magnetic resonance imaging. For the first time, a facile, modified solvent diffusion method is used for the co‐encapsulation of both an anticancer drug and near‐infrared dyes. The resulting folate‐derivatized theranostics nanoparticles could allow for targeted optical/magnetic resonance imaging and targeted killing of folate‐expressing cancer cells.
Scoping software process lines
Authors: Armbrust Ove , Katahira Masafumi , Miyamoto Yuko , Münch Jürgen , Nakao Haruka , Ocampo Alexis 
Published: April 2009

AbstractDefining organization‐specific process standards by integrating, harmonizing, and standardizing heterogeneous and often implicit processes is an important task, especially for large development organizations. On the one hand, such a standard must be generic enough to cover all of the organization's development activities; on the other hand, it must be as detailed and precise as possible to support employees' daily work. Today, organizations typically maintain and advance a plethora of individual processes, each addressing specific problems. This requires enormous effort, which could be spent more efficiently. This article introduces an approach for developing a Software Process Line that, similar to a Software Product Line, promises to reduce the complexity and thus, the effort required for managing the processes of a software organization. We propose Scoping, Modeling, and Architecting the Software Process Line as major steps, and describe in detail the Scoping approach we recommend, based on an analysis of the potential products to be produced in the future, the projects expected in the future, and the respective process capabilities needed. In addition, the article sketches experience from determining the scope of space process standards for satellite software development. Finally, it discusses the approach, draws conclusions, and gives an outlook on future work. Copyright © 2009 John Wiley & Sons, Ltd.
Method engineering: towards methods as services
Authors: Rolland Colette 
Published: April 2009

AbstractMethod engineering has emerged as the result of the necessity to adapt methods to better fit the needs of the development task at hand. Its aim is to provide techniques for retrieving reusable method components, adapting and assembling these together to form the new method. The paper provides a survey of the main results obtained for the two issues of defining and assembling components. It argues, thereafter, that the full power of method components can be widely exploited by moving to the notion of method services. The paper finally outlines a possible approach towards Method as a Service (MaaS), and illustrates it. Copyright © 2009 John Wiley & Sons, Ltd.