bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of the metabolic/redox state, histone gene switching, DNA replication and S-phase progression by moonlighting metabolic enzymes
Authors: He Hongpeng , Lee Mei-Chin , Zheng Li-Ling , Zheng Lei , Luo Yan
Published: November 2012

The concept of one-protein–multiple-function, i.e. moonlighting proteins, is an ever-expanding paradigm. We obtained compelling evidence that an array of ‘cytoplasmic’ metabolic enzymes can enter the nuclei to carry out moonlighting transcription functions; this phenomenon is conserved from Drosophila to humans. Of particular interest are the classical glycolytic enzymes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and LDH (lactate dehydrogenase), which utilize NAD(H) as coenzymes and not only moonlight (in their nuclear forms) to regulate the transcription of S-phase-specific histone genes, but also act as metabolic/redox sensors that link histone gene switching to DNA replication and S-phase progression.
Regulation of protein phosphatase 1 by intrinsically disordered proteins
Authors: Choy Meng S. , Page Rebecca , Peti Wolfgang
Published: November 2012

PP1 (protein phosphatase 1) is an essential serine/threonine phosphatase that plays a critical role in a broad range of biological processes, from muscle contraction to memory formation. PP1 achieves its biological specificity by forming holoenzymes with more than 200 known regulatory proteins. Interestingly, most of these regulatory proteins (≥70%) belong to the class of IDPs (intrinsically disordered proteins). Thus structural studies highlighting the interaction of these IDP regulatory proteins with PP1 are an attractive model system because it allows general parameters for a group of diverse IDPs that interact with the same binding partner to be identified, while also providing fundamental insights into PP1 biology. The present review provides a brief overview of our current understanding of IDP–PP1 interactions, including the importance of pre-formed secondary and tertiary structures for PP1 binding, as well as changes of IDP dynamics upon interacting with PP1.
Possible involvement of the relationship of LRRK2 and autophagy in Parkinson's disease
Authors: Bravo-San Pedro José M. , Gómez-Sánchez Rubén , Niso-Santano Mireia , Pizarro-Estrella Elisa , González-Polo Rosa A. , Fuentes José M.
Published: November 2012

PD (Parkinson's disease) is a neurodegenerative disorder caused by loss of dopamine-generating cells in the substantia nigra. The implication of genetic factors in the aetiology of PD has an essential importance in our understanding of the development of the disease. Mutations in the LRRK2 (leucine-rich repeat kinase 2) gene cause late-onset PD with a clinical appearance indistinguishable from idiopathic PD. Moreover, LRRK2 has been associated with the process of autophagy regulation. Autophagy is an intracellular catabolic mechanism whereby a cell recycles or degrades damaged proteins and cytoplasmic organelles. In the present paper, we discuss the role of LRRK2 in autophagy, and the importance of this relationship in the development of nigral degeneration in PD.
LEA proteins: IDPs with versatile functions in cellular dehydration tolerance
Authors: Hincha Dirk K. , Thalhammer Anja
Published: November 2012

LEA (late embryogenesis abundant) proteins were originally described almost 30 years ago as accumulating late in plant seed development. They were later found to be induced in vegetative plant tissues under environmental stress conditions and also in desiccation-tolerant micro-organisms and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Most LEA proteins are predicted to be intrinsically disordered and this has been experimentally verified in several cases. In addition, some LEA proteins partially fold, mainly into α-helices, during drying or in the presence of membranes. Recent studies have concentrated on the potential roles of LEA proteins in stabilizing membranes or sensitive enzymes during freezing or drying, and the present review concentrates on these two possible functions of LEA proteins in cellular dehydration tolerance.
The synaptic function of LRRK2
Authors: Lee Seongsoo , Imai Yuzuru , Gehrke Stephan , Liu Song , Lu Bingwei
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) are the most frequent genetic lesions so far found in familial as well as sporadic forms of PD (Parkinson's disease), a neurodegenerative disease characterized by the dysfunction and degeneration of dopaminergic and other neuronal types. The molecular and cellular mechanisms underlying LRRK2 action remain poorly defined. Synaptic dysfunction has been increasingly recognized as an early event in the pathogenesis of major neurological disorders. Using Drosophila as a model system, we have shown that LRRK2 controls synaptic morphogenesis. Loss of dLRRK (Drosophila LRRK2) results in synaptic overgrowth at the Drosophila neuromuscular junction synapse, whereas overexpression of wild-type dLRRK, hLRRK2 (human LRRK2) or the pathogenic hLRRK2-G2019S mutant has the opposite effect. Alteration of LRRK2 activity also affects synaptic transmission in a complex manner. LRRK2 exerts its effects on synaptic morphology by interacting with distinct downstream effectors at the pre- and post-synaptic compartments. At the postsynapse, LRRK2 functionally interacts with 4E-BP (eukaryotic initiation factor 4E-binding protein) and the microRNA machinery, both of which negatively regulate protein synthesis. At the presynapse, LRRK2 phosphorylates and negatively regulates the microtubule-binding protein Futsch and functionally interacts with the mitochondrial transport machinery. These results implicate compartment-specific synaptic dysfunction caused by altered protein synthesis, cytoskeletal dynamics and mitochondrial transport in LRRK2 pathogenesis and offer a new paradigm for understanding and ultimately treating LRRK2-related PD.
Phosphorylation of LRRK2: from kinase to substrate
Authors: Lobbestael Evy , Baekelandt Veerle , Taymans Jean-Marc
Published: November 2012

The PD (Parkinson's disease) protein LRRK2 (leucine-rich repeat kinase 2) occurs in cells as a highly phosphorylated protein, with the majority of phosphosites clustering in the region between the ankyrin repeat and leucine-rich repeat domains. The observation that several pathogenic variants of LRRK2 display strongly reduced cellular phosphorylation suggests that phosphorylation of LRRK2 is involved in the PD pathological process. Furthermore, treatment of cells with inhibitors of LRRK2 kinase activity, which are currently considered as potential disease-modifying therapeutics for PD, leads to a rapid decrease in the phosphorylation levels of LRRK2. For these reasons, understanding the cellular role and regulation of LRRK2 as a kinase and as a substrate has become the focus of intense investigation. In the present review, we discuss what is currently known about the cellular phosphorylation of LRRK2 and how this relates to its function and dysfunction.
Insights into LRRK2 function and dysfunction from transgenic and knockout rodent models
Authors: Sloan Maximilian , Alegre-Abarrategui Javier , Wade-Martins Richard
Published: November 2012

Mutations in the LRRK2 (leucine-rich repeat kinase 2) gene on chromosome 12 cause autosomal dominant PD (Parkinson's disease), which is indistinguishable from sporadic forms of the disease. Numerous attempts have therefore been made to model PD in rodents via the transgenic expression of LRRK2 and its mutant variants and to elucidate the function of LRRK2 by knocking out rodent Lrrk2. Although these models often only partially recapitulate PD pathology, they have helped to elucidate both the normal and pathological function of LRRK2. In particular, LRRK2 has been suggested to play roles in cytoskeletal dynamics, synaptic machinery, dopamine homoeostasis and autophagic processes. Our understanding of how these pathways are affected, their contribution towards PD development and their interaction with one another is still incomplete, however. The present review summarizes the findings from LRRK2 rodent models and draws potential connections between the apparently disparate cellular processes altered, in order to better understand the underlying mechanisms of LRRK2 dysfunction and illuminate future therapeutic interventions.
Biochemical and functional characterization of the ROC domain of DAPK establishes a new paradigm of GTP regulation in ROCO proteins
Authors: Bialik Shani , Kimchi Adi
Published: November 2012

DAPK (death-associated protein kinase) is a newly recognized member of the mammalian family of ROCO proteins, characterized by common ROC (Ras of complex proteins) and COR (C-terminal of ROC) domains. In the present paper, we review our recent work showing that DAPK is functionally a ROCO protein; its ROC domain binds and hydrolyses GTP. Furthermore, GTP binding regulates DAPK catalytic activity in a novel manner by enhancing autophosphorylation on inhibitory Ser308, thereby promoting the kinase ‘off’ state. This is a novel mechanism for in cis regulation of kinase activity by the distal ROC domain. The functional similarities between DAPK and the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat protein kinase 2), another member of the ROCO family, are also discussed.
Cellular effects of LRRK2 mutations
Authors: Cookson Mark R.
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) are a relatively common cause of inherited PD (Parkinson's disease), but the mechanism(s) by which mutations lead to disease are poorly understood. In the present paper, I discuss what is known about LRRK2 in cellular models, focusing specifically on assays that have been used to tease apart the effects of LRRK2 mutations on cellular phenotypes. LRRK2 expression has been suggested to cause loss of neuronal viability, although because it also has a strong effect on the length of neurites on these cells, whether this is true toxicity or not is unclear. Also, LRRK2 mutants can promote the redistribution of LRRK2 from diffuse cytosolic staining to more discrete structures, at least at high expression levels achieved in transfection experiments. The relevance of these phenotypes for PD is not yet clear, and a great deal of work is needed to understand them in more depth.
Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins
Authors: Tamiola Kamil , Mulder Frans A.A.
Published: November 2012

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.
Native disorder mediates binding of dynein to NudE and dynactin
Authors: Barbar Elisar
Published: November 2012

In the present paper, I report the molecular overlap of the linkage of three essential protein complexes that co-ordinate the formation of the mitotic spindle. These proteins are dynein, a large motor complex that moves machinery inside cells, and two of its regulators: a protein complex called dynactin, a dynein activator, and a protein called NudE whose depletion in mice produces a small brain and mental retardation. What is intriguing about the dynein–dynactin–NudE interplay is that dynactin and NudE bind to a common segment of dynein that is intrinsically disordered. Elucidating differences in their binding modes may explain how one regulator can be selected over the other even when both are present in the same cellular compartment. These results not only have a far-reaching impact on our understanding of processes essential for the formation and orientation of the spindle, but also offer a novel role for protein disorder in controlling cellular processes, and highlight the advantages of NMR spectroscopy in elucidating atomic-level characterization of extremely complex dynamic cellular assemblies.
Intrinsically disordered proteins: administration not executive
Authors: Williamson Mike P. , Potts Jennifer R.
Published: November 2012

IDPs (intrinsically disordered proteins) are common in eukaryotic genomes and have regulatory roles. In the cell, they are disordered, although not completely random. They bind weakly, but specifically, often remaining partially disordered even when bound. Whereas folded globular proteins have ‘executive’ roles in the cell, IDPs have an essential administrative function, making sure that the executive functions are properly co-ordinated. This makes them a good target for pharmaceutical intervention.
Development of inhibitors as research tools for carbohydrate-processing enzymes
Authors: Gloster Tracey M.
Published: November 2012

Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.
Hans Adolph Buchdahl 1919 - 2010
Authors: Melrose D. B.
Published: November 2012

Hans Buchdahl, who died in Adelaide on 7 January 2010 at the age of 90, contributed extensively to three fields of theoretical physics: geometric optics, general relativity and thermodynamics. His early work on optical aberration coefficients was motivated by a wartime need; through this work he rejuvenated a field that had been moribund for close to a century. The methods he developed underlie some of the modern analytic and numerical approaches to the design of optical instruments. He contributed to the general theory of relativity during what was known as its ?Golden Age', and he made pedagogic contributions to the discipline of thermodynamics.
Ernest Oliver Tuck 1939 - 2009
Authors: Grimshaw Roger
Published: November 2012

Ernie Tuck was one of Australia's most outstanding applied mathematicians, with an international reputation as a leading authority on water waves and ship hydrodynamics. He made seminal and incisive theoretical analyses in many areas, especially on wave resistance of slender ships and wave interaction with obstacles. His work is characterized by his ability to find the essentials of a complex problem, and then to apply apparently simple, but revealing analyses, using a combination of perturbation and asymptotic techniques with numerical calculations. He was an outstanding expositor, supervised twenty-five doctoral students, and will be remembered by his many colleagues as a brilliant scientist and an enthusiastic and caring person.
John Paul Wild 1923 - 2008
Authors: Frater R. H. , Ekers R. D.
Published: November 2012

Paul Wild stands tall among the founding fathers of modern radio astronomy. His early work became the foundation for all future research on solar radio bursts. He established the theory and identified the different types of radio bursts. He developed new types of instrument including the dynamic spectrograph and a radioheliograph to make two-dimensional movie images. His early interest in the radio spectrum of hydrogen led to analysis of the hyperfine structure of hydrogen emission and a publication that became a classic paper in the field. Recognition that the 21 cm hydrogen line could be used to measure the Zeeman effect and through that magnetic fields in astronomical sources was another key contribution to modern astronomy. He became Chief of the CSIRO Division of Radiophysics and developed and demonstrated an outstanding microwave landing system for aviation. As Chairman of CSIRO he led the organization through a major restructuring and adapted CSIRO to bring it closer to industry while maintaining a high standard of excellence and originality. Throughout his career, Paul Wild provided great leadership at all levels of science in Australia.
Ca intercalated bilayer graphene as a thinnest limit of superconducting C
6
Ca
Authors: Kanetani Kohei , Sugawara Katsuaki , Sato Takafumi , Shimizu Ryota , Iwaya Katsuya , Hitosugi Taro , Takahashi Takashi
Published: November 2012

Success in isolating a 2D graphene sheet from bulky graphite has triggered intensive studies of its physical properties as well as its application in devices. Graphite intercalation compounds (GICs) have provided a platform of exotic quantum phenomena such as superconductivity, but it is unclear whether such intercalation is feasible in the thinnest 2D limit (i.e., bilayer graphene). Here we report a unique experimental realization of 2D GIC, by fabricating calcium-intercalated bilayer graphene C
6
CaC
6
on silicon carbide. We have investigated the structure and electronic states by scanning tunneling microscopy and angle-resolved photoemission spectroscopy. We observed a free-electron–like interlayer band at the Brillouin-zone center, which is thought to be responsible for the superconductivity in 3D GICs, in addition to a large π* Fermi surface at the zone boundary. The present success in fabricating Ca-intercalated bilayer graphene would open a promising route to search for other 2D superconductors as well as to explore its application in devices.
MAPK phosphatase-1 is required for regulatory natural autoantibody-mediated inhibition of TLR responses
Authors: Grönwall Caroline , Chen Yifang , Vas Jaya , Khanna Sahil , Thiel Steffen , Corr Maripat , Kono Dwight H. , Silverman Gregg J.
Published: November 2012

Naturally arising IgM antibodies, which recognize neo-determinants on apoptotic cell (AC) membranes, are present from birth and can be further induced by AC challenge. Such naturally arising IgM antibodies can suppress proinflammatory responses to purified agonists for Toll-like receptors (TLRs), as well as block the induction of IgG immune complex-induced in vitro and in vivo pathogenic responses. To investigate the responsible mechanisms, we studied the regulatory effects of IgM anti-AC antibody on responses in bone marrow-derived dendritic cells mediated by a range of different TLRs and found that addition of IgM anti-AC inhibited the activation of the primary MAPKs: ERK1/2, JNK, and particularly p38. This was dependent on the recruitment of either C1q or mannose-binding lectin, which are both early complement factors that tag ACs for innate immune recognition. Strikingly, MAPK inhibition of responses to TLR agonists, and to lupus IgG autoantibody-chromatin immune complexes, was found to correlate with, and had an absolute requirement for, the induction and nuclear localization of MAPK phosphatase-1, a factor known to mediate glucocorticoid suppression of immune responses. Further experiments showed that natural IgM antibodies in serum exhibited the same inhibitory properties. These studies elucidate a novel homeostatic pathway by which natural antibodies, which are products of the adaptive immune system, can directly blunt inflammatory responses by recruitment and coordination of a primitive regulatory pathway of the innate immune system.
The effects of valence‐based and discrete emotional states on aesthetic response
Authors: Cheng Yin‐Hui
Published: November 2012

There is increasing recognition that consumer aesthetics—the responses of consumers to the aesthetic or appearance aspects of products—has become an important area of marketing in recent years. Consumer aesthetic responses to a product are a source of pleasure for the consumer. Previous research into the aesthetic responses to products has often emphasized exterior factors and visual design, but studies have seldom considered the psychological aesthetic experience of consumers, and in particular their emotional state. This study attempts to bridge this gap by examining the link between consumers’ emotions and their aesthetic response to a product. Thus, the major goal of this study was to determine how valence‐based and discrete emotional states influence choice. In Studies 1 and 2, positive and negative emotions were manipulated to implement two different induction techniques and explore the effect of emotions on participants’ choices in two separate experiments. The results of both experiments confirmed the predictions, indicating that aesthetic responses and purchase intention are functions of emotional valence, such that both are stronger for people in a positive emotional state than for those in a negative emotional state. Study 2 also used a neutral affective state to establish the robustness of this observed effect of incidental affect. The results of Study 3 demonstrate that aesthetic response and purchase intention are not only a function of affect valence, but also are affected by the certainty appraisal associated with specific affective states. This research, therefore, contributes to the literature by offering empirical evidence that incidental affect is a determinant of aesthetic response.
Fabrication, structure and magnetic properties of CoPt3, CoPt and Co3Pt nanoparticles
Authors: Wang Yaxin , Zhang Xiaolong , Liu Yang , Jiang Yuhong , Zhang Yongjun , Wang Jingshu , Liu Yanqing , Liu Huilian , Sun Yunfei , S D Beach Geoffrey , Yang Jinghai
Published: November 2012

A set of Co
x
Pt100−x
nanoparticles (NPs) was synthesized by the sol–gel method. The structure and magnetic properties of the produced samples were investigated by x-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED) and a vibrating sample magnetometer. When the Co content ranged from 25 to 75 at%, the results of XRD, HRTEM and SAED revealed the formation of L12 CoPt3, L10 CoPt and face-centred cubic Co3Pt NPs. Magnetic measurements indicated that CoPt3 and Co3Pt had soft magnetic properties. When the Co composition was 50 at%, the sample coercivity reached a giant value of ∼470 kA m−1.
Optical behaviour of thick gold and silver films with periodic circular nanohole arrays
Authors: Hajiaboli Ahmadreza , Kahrizi Mojtaba , Truong Vo-Van
Published: November 2012

To better understand the enhanced optical transmission observed with an array of nanoholes on optically thick metallic films, an extensive numerical calculation is presented in this paper to relate the scattering modes observed to transmittance spectral behaviour. Surface plasmon polariton Bloch waves, Wood's anomalies and localized surface plasmon resonances at the rim of the nanoholes are investigated based on scattering modes that form the features of the transmission spectrum. The finite difference time-domain method is applied to calculate the transmission intensity from films of gold and silver subjected to variations in geometrical parameters such as film thickness, spatial period of the structures and hole diameter. Analysis of transmission spectra showed that the cut-off frequency of the array of subwavelength holes is mostly defined by the thickness of the film and the diameter of the holes rather than the periodicity of the structures.
Anion dynamics in the first 10 milliseconds of an argon–acetylene radio-frequency plasma
Authors: van de Wetering F M J H , Beckers J , Kroesen G M W
Published: November 2012

The time evolution of the smallest anions (C2H− and H2CC−), just after plasma ignition, is studied by means of microwave cavity resonance spectroscopy (MCRS) in concert with laser-induced photodetachment under varying gas pressure and temperature in an argon–acetylene radio-frequency (13.56 MHz) plasma. These anions act as an initiator for spontaneous dust particle formation in these plasmas. With an intense 355 nm Nd : YAG laser pulse directed through the discharge, electrons are detached only from these anions present in the laser path. This results in a sudden increase in the electron density in the plasma, which can accurately and with sub-microsecond time resolution be measured with MCRS. By adjusting the time after plasma ignition at which the laser is fired through the discharge, the time evolution of the anion density can be studied. We have operated in the linear regime: the photodetachment signal is proportional to the laser intensity. This allowed us to study the trends of the photodetachment signal as a function of the operational parameters of the plasma. The density of the smallest anions steadily increases in the first few milliseconds after plasma ignition, after which it reaches a steady state. While keeping the gas density constant, increasing the gas temperature in the range 30–120 °C limits the number of smallest anions and saturates at a temperature of about 90 °C. A reaction pathway is proposed to explain the observed trends.
Micromagnetic study of exchange spring media with a rough interface on an example of FePt films
Authors: Dymerska Barbara , Lee Jehyun , Fidler Josef , Suess Dieter
Published: November 2012

In this paper exchange spring media with a rough interface between magnetically hard and soft materials are considered. As an example a nanostructure of FePt L10/A1 films is analysed. The observed features, such as inclusions of L10 phase in A1 matrix, were transferred into finite element numerical models. Also, the distribution of the hard phase along the thickness of the medium was analysed. It was found to fit linear, logistic and quadratic functions in the interface region. Micromagnetic simulations show that the position and size of obstacles significantly alter the switching field of the media. Moreover, the minimal switching field of H
sw = 0.9 T was observed for a quadratic L10 distribution in an 18 nm thick interface region. The numerical results agree well with an analytical formula of the pinning field of exchange spring media, which is derived for the general case of spatially varying magnetization, anisotropy and exchange constant. It is emphasized that the applicability of the numerical methods described here is not limited to FePt L10/A1 films but could be interesting also for other exchange spring media, such as CoPt L10/A1 or FePt(L10)/FeAu(L10).
Infrared spectroscopy characterization of 3C–SiC epitaxial layers on silicon
Authors: Pluchery Olivier , Costantini Jean-Marc
Published: November 2012

We have measured the transmission Fourier transform infrared spectra of cubic silicon carbide (3C–SiC polytype) epitaxial layer with a 20 µm thickness on a 200 µm thick silicon substrate. Spectra were recorded in the 400–4000 cm−1 wavenumber range. A novel approach of IR spectra computations based on the recursion capability of the C programming language is presented on the basis of polarized light propagation in layered media using generalized Fresnel's equations. The complex refractive indices are the only input parameters. A remarkable agreement is found between all of the experimental SiC and Si spectral features and the calculated spectra. A comprehensive assignment of (i) the two fundamental transverse optical (TO) (790 cm−1) and longitudinal optical (LO) (970 cm−1) phonon modes of 3C–SiC, (ii) with their overtones (1522–1627 cm−1) and (iii) the two-phonon optical-acoustical summation bands (1311–1409 cm−1) is achieved on the basis of available literature data. This approach allows sorting out the respective contributions of the Si substrate and SiC upper layer. Such calculations can be applied to any medium, provided that the complex refractive index data are known.
Free-electron absorption in n-doped GaN semiconductors at mid-IR wavelengths in the strong phonon–plasmon coupling regime
Authors: Shkerdin G , Rabbaa S , Stiens J , Vounckx R
Published: November 2012

We have calculated the free-carrier absorption coefficient for polar III–V semiconductors with strong LO phonon–plasmon interaction. We took several mechanisms into account, which assist in the photon absorption process. At the considered doping concentrations the most important scattering mechanisms are thermal LO phonon branch scattering, impurity scattering, plasmon branch scattering and acoustic phonon scattering. For all these interaction potentials screening by conduction electrons has been included. Computations are performed for β-GaN and α-GaN doped semiconductors at different mid-IR wavelengths and doping concentrations. For all considered cases the relative difference between the Drude model calculation results based on static and dynamic damping factors is typically smaller than 25–30%.
Mechanisms for ion-irradiation-induced relaxation of stress in mosaic structured Cu thin films
Authors: Fu E G , Wang Y Q , Nastasi M
Published: November 2012

In this paper, helium (He) ion irradiations with various fluences were performed on sputtered Cu thin films with a mosaic structure to evolve biaxial stress. X-ray diffraction of the θ–2θ method was used to determine the residual strains in the thin films by measuring the spacing of the crystallographic planes. The results show the in-plane biaxial tensile stress has been reduced by ion irradiation. A new proposed model is discussed to explain the ion-irradiation-induced stress release in mosaic structured Cu thin films.
Numerical computation of Thomson scattering spectra for non-Maxwellian or anisotropic electron distribution functions
Authors: Pastor I. , Guasp J. , Álvarez-Estrada R.F. , Castejón F.
Published: November 2012

Monte Carlo techniques applied to Thomson scattering (TS) power spectrum computation have been extended so as to include non-Maxwellian and anisotropic electron distribution functions (EDFs). First, a simple model has been selected for the spatial (angular) anisotropy of electron velocities (uniformly distributed around an axis of angular symmetry on a cone of semiaperture θ
anis), while the energies are distributed according to a lower-hybrid-like model function. Spectra have been computed, and their dependence with the EDF model parameters has been given. The most noticeable changes in the spectrum with respect to the isotropic Maxwellian are the broadening and blue-shift of the spectrum due to suprathermal electrons, and the presence of satellite or additional maxima (that can be either red-shifted or blue-shifted with respect to the thermal Maxwellian maximum) coming from the anisotropy of the EDF. Also, extensive numerical computations have been carried out on angularly non-separable EDFs (meaning that the sampling of the distribution function cannot be done independently on angle and energy variables), like the relativistic bi-Maxwellian (with or without drift). The connection of these results with some recent TS measurements reported by Yamada et al (2010 Rev. Sci. Instrum.
81 10D522) and more generally, with the possibility of detecting non-Maxwellian or anisotropic EDF features with TS, has been discussed.
The structure of a thermostable mutant of pro-papain reveals its activation mechanism
Authors: Roy Sumana , Choudhury Debi , Aich Pulakesh , Dattagupta Jiban K. , Biswas Sampa
Published: November 2012

Papain is the archetype of a broad class of cysteine proteases (clan C1A) that contain a pro-peptide in the zymogen form which is required for correct folding and spatio-temporal regulation of proteolytic activity in the initial stages after expression. This study reports the X-ray structure of the zymogen of a thermostable mutant of papain at 2.6 Å resolution. The overall structure, in particular that of the mature part of the protease, is similar to those of other members of the family. The structure provides an explanation for the molecular basis of the maintenance of latency of the proteolytic activity of the zymogen by its pro-segment at neutral pH. The structural analysis, together with biochemical and biophysical studies, demonstrated that the pro-segment of the zymogen undergoes a rearrangement in the form of a structural loosening at acidic pH which triggers the proteolytic activation cascade. This study further explains the bimolecular stepwise autocatalytic activation mechanism by limited proteolysis of the zymogen of papain at the molecular level. The possible factors responsible for the higher thermal stability of the papain mutant have also been analyzed.
ScrewFit: combining localization and description of protein secondary structure
Authors: Calligari Paolo A. , Kneller Gerald R.
Published: November 2012

A new application of theScrewFitalgorithm [Kneller & Calligari (2006),Acta Cryst.D62, 302–311] is presented which adds the detection of protein secondary-structure elements to their detailed geometrical description in terms of a curve with intrinsic torsion. The extension is based on confidence and persistence criteria for theScrewFitparameters which are established by analyzing the structural fluctuations of standard motifs in the SCOP fold classes. The agreement with the widely usedDSSPmethod is comparable with the general consensus among other methods in the literature. This combination of secondary-structure detection and analysis is illustrated for the enzyme adenylate kinase.
Structure of the catalytic domain of theSalmonellavirulence factor SseI
Authors: Bhaskaran Shyam S. , Stebbins C. Erec
Published: November 2012

SseI is secreted into host cells bySalmonellaand contributes to the establishment of systemic infections. The crystal structure of the C-terminal domain of SseI has been solved to 1.70 Å resolution, revealing it to be a member of the cysteine protease superfamily with a catalytic triad consisting of Cys178, His216 and Asp231 that is critical to its virulence activities. Structure-based analysis revealed that SseI is likely to possess either acyl hydrolase or acyltransferase activity, placing this virulence factor in the rapidly growing class of enzymes of this family utilized by bacterial pathogens inside eukaryotic cells.
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels
Authors: Bibby Jaclyn , Keegan Ronan M. , Mayans Olga , Winn Martyn D. , Rigden Daniel J.
Published: November 2012

Proteinab initiomodels predicted from sequence data alone can enable the elucidation of crystal structures by molecular replacement. However, the calculation of suchab initiomodels is typically computationally expensive. Here, a computational pipeline based on the clustering and truncation of cheaply obtainedab initiomodels for the preparation of structure ensembles is described. Clustering is used to select models and to quantitatively predict their local accuracy, allowing rational truncation of predicted inaccurate regions. The resulting ensembles, with or without rapidly added side chains, solved 43% of all test cases, with an 80% success rate for all-α proteins. A program implementing this approach,AMPLE, is included in theCCP4 suite of programs. It only requires the input of aFASTAsequence file and a diffraction data file. It carries out the modelling using locally installedRosetta, creates search ensembles and automatically performs molecular replacement and model rebuilding.
Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa
Authors: Nguyen Bich Ngan , Moeyaert Benjamien , Van Hecke Kristof , Dedecker Peter , Mizuno Hideaki , Hofkens Johan , Van Meervelt Luc
Published: November 2012

The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain β-strands caused by oligomerization along theACinterface.
Measurement of detergent concentration using 2,6-dimethylphenol in membrane-protein crystallization
Authors: Prince Chelsy , Jia Zongchao
Published: November 2012

Methods have previously been developed to measure detergent concentration in membrane-protein samples, but most have significant limitations, such as requiring specialized equipment or consuming a significant amount of precious sample. This work explores the use of 2,6-dimethylphenol in a phenol–sulfuric acid assay to accurately measure the concentration of common glycosidic-based detergents used in crystallization. This method is amenable to routine laboratory use, provides excellent sensitivity and significantly reduces the sample volume required. Using anEscherichia colityrosine kinase (Etk) construct as an example, it is shown that the crystallization potential of Etk is directly influenced by measurable changes in detergent concentration.
Structural insights into the specific anti-HIV property of actinohivin: structure of its complex with the α(1–2)mannobiose moiety of gp120
Authors: Hoque M. Mominul , Suzuki Kaoru , Tsunoda Masaru , Jiang Jiandong , Zhang Fang , Takahashi Atsushi , Ohbayashi Naomi , Zhang Xiaoxue , Tanaka Haruo , Ōmura Satoshi , Takénaka Akio
Published: November 2012

Actinohivin (AH) is an actinomycete lectin with a potent specific anti-HIV activity. In order to clarify the structural evidence for its specific binding to the α(1–2)mannobiose (MB) moiety of the D1 chains of high-mannose-type glycans (HMTGs) attached to HIV-1 gp120, the crystal structure of AH in complex with MB has been determined. The AH molecule is composed of three identical structural modules, each of which has a pocket in which an MB molecule is bound adopting a bracket-shaped conformation. This conformation is stabilized through two weak C—H...O hydrogen bonds facilitated by the α(1–2) linkage. The binding features in the three pockets are quite similar to each other, in accordance with the molecular pseudo-threefold symmetry generated from the three tandem repeats in the amino-acid sequence. The shape of the pocket can accept two neighbouring hydroxyl groups of the O3and O4atoms of the equatorial configuration of the second mannose residue. To recognize these atoms through hydrogen bonds, an Asp residue is located at the bottom of each pocket. Tyr and Leu residues seem to block the movement of the MB molecules. Furthermore, the O1atom of the axial configuration of the second mannose residue protrudes from each pocket into an open space surrounded by the conserved hydrophobic residues, suggesting an additional binding site for the third mannose residue of the branched D1 chain of HMTGs. These structural features provide strong evidence indicating that AH is only highly specific for MB and would facilitate the highly specific affinity of AH for any glycoprotein carrying many HMTGs, such as HIV-1 gp120.
Dimeric structure of the N-terminal domain of PriB protein fromThermoanaerobacter tengcongensissolvedab initio
Authors: Liebschner Dorothee , Brzezinski Krzysztof , Dauter Miroslawa , Dauter Zbigniew , Nowak Marta , Kur Józef , Olszewski Marcin
Published: November 2012

PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacteriumThermoanaerobacter tengcongensis(TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain ofT. tengcongensisshows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains,TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains ofTtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.
Electronic structure and hybridization of CaS by means of X-ray absorption spectroscopy at Ca and S K-edges
Authors: Xu Wei , Liu Lijuan , Cui Mingqi , Zheng Lei , Hu Yongfeng , Marcelli Augusto , Wu Ziyu
Published: November 2012

The cubic calcium sulfide (CaS) is a well known system and an attractive building block material for many luminescence technological applications. However, it is essential to achieve an accurate understanding of its electronic structure in order to engineer its band structure for optimized applications. Here a study of the electronic structure of CaS by means of X-ray absorption spectroscopy performed at both Ca and SK-edges, and calculations performed in the framework of the multiple-scattering theory and of the finite difference method are presented. At the CaK-edge the presence of an anomalousdstates feature is discussed while in the SK-edge spectrum the presence of a pre-edge shoulder owing to the hybridization among Cadstates and Spstates is pointed out. Although thel-projected density of states of CaS is in good agreement with previous first-principles calculations, the standard muffin-tin potential is inadequate to reproduce near-edge structures at both Ca and SK-edges in this system. Indeed, with its highly symmetric and less compact structure, CaS is characterized by a large set of collinear atomic configurations that pose severe constraints on the construction of the atomic potential. On the contrary, the finite-difference method with no muffin-tin approximation is more suitable for X-ray absorption calculations in this system.
Prediction of fatigue life of high-heat-load components made of oxygen-free copper by comparing with Glidcop
Authors: Takahashi Sunao , Sano Mutsumi , Watanabe Atsuo , Kitamura Hideo
Published: November 2012

Following a successful study on the prediction of fatigue life of high-heat-load components made of Glidcop, the thermal limitation of oxygen-free copper (OFC), which is used more commonly than Glidcop, has been studied. In addition to its general mechanical properties, the low-cycle-fatigue (LCF) and creep properties of OFC were investigated in detail and compared with those of Glidcop. The breaking mode of OFC, which was observed to be completely different from that of Glidcop in a fatigue fracture experiment, clarified the importance of considering the creep–fatigue interaction. An additional LCF test with compressive strain holding was conducted so that the creep–fatigue life diagram for out-of-phase thermal fatigue could be obtained on the basis of the strain-range partitioning method. The life predicted from elasto-plastic creep analysis agreed well with that determined from the void ratio estimated in the fatigue fracture experiment.
Towards high-resolution synchrotron radiation imaging with statistical iterative reconstruction
Authors: Rashed Essam A. , Kudo Hiroyuki
Published: November 2012

Synchrotron radiation (SR) X-ray micro-computed tomography (CT) is an effective imaging modality for high-resolution investigation of small objects, with several applications in medicine, biology and industry. However, the limited size of the detector field of view (FOV) restricts the sample dimensions to only a few millimeters. When the sample size is larger than the FOV, images reconstructed using conventional methods suffer from DC-shift and low-frequency artifacts. This classical problem is known as the local tomography or the interior problem. In this paper, a statistical iterative reconstruction method is introduced to eliminate image artifacts resulting from the local tomography. The proposed method, which can be used in several SR imaging applications, enables high-resolution SR imaging with superior image quality compared with conventional methods. Real data obtained from different SR micro-CT applications are used to evaluate the proposed method. Results indicate a noteworthy quality improvement in the image reconstructed from the local tomography measurements.
Two-dimensional resonant magnetic soft X-ray scattering set-up for extreme sample environment
Authors: Stanescu Stefan , Mocuta Cristian , Merlet Frederic , Barbier Antoine
Published: November 2012

The newly built MagSAXS (magnetic small-angle X-ray scattering) set-up dedicated to the direct two-dimensional measurement of magnetic scattering using polarized synchrotron radiation in extreme sample environments is presented. Pure optical transport of the image is used to record the magnetic scattering with a two-dimensional CCD visible-light camera. The set-up is able to probe magnetic correlation lengths from the micrometer down to the nanometer scale. A detailed layout is presented along with preliminary results obtained at several beamlines at Synchrotron SOLEIL. The presented examples underline the wide range of possible applications spanning from correlation lengths determination to Fourier transform holography.
Concepts for flexible and efficient monochromatization of X-rays by refraction to a relative bandwidth of the order of 0.5%
Authors: Jark Werner
Published: November 2012

Recently it was shown experimentally that regular arrays of tiny prisms can be used as X-ray monochromators providing a spectral bandwidth of below 2%. Successively the measured spectral transmission functions of monochromators operated under different conditions were found to be in agreement with expectations within an analytical model. This type of monochromator focuses chromatically and thus necessitates the use of an exit slit for the monochromatization. This contribution will show that the lower limit for the achievable bandpass can be predicted under practically feasible experimental conditions. Refractive monochromators based on prism arrays are found to be feasible solutions for monochromatization with high transmission to a spectral bandwidth of the order of 0.5%. The bandwidth can easily be increased by adjusting the exit slit setting accordingly. Consequently, the presented refractive devices would make for tunable monochromators with tunable bandwidth, which provides more flexibility for an intermediate bandwidth of <1%, which multilayer monochromators have difficulty providing routinely.