Electron dephasing near zero temperature: an experimental review

The behavior of the electron dephasing time near zero temperature, $\tau_\phi^0$, has recently attracted vigorous attention. This renewed interest is primarily concerned with whether $\tau_\phi^0$ should reach a finite or an infinite value as $T \to$ 0. While it is accepted that $\tau_\phi^0$ should diverge if there exists only electron-electron (electron-phonon) scattering, several recent measurements have found that $\tau_\phi^0$ depends only very weakly on temperature, if at all, when $T$ is sufficiently low. This article discusses the current experimental status of "the saturation problem", and concludes that the origin(s) for this widely observed saturation are still unresolved

Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings

Characterization of segmental flexibility is needed to understand the biological mechanisms of the very large category of functionally diverse proteins, exemplified by the regulators of complement activation, that consist of numerous compact modules or domains linked by short, potentially flexible, sequences of amino acid residues. The use of NMR-derived residual dipolar couplings (RDCs), in magnetically aligned media, to evaluate interdomain motion is established but only for two-domain proteins. We focused on the three N-terminal domains (called CCPs or SCRs) of the important complement regulator, human factor H (i.e. FH1-3). These domains cooperate to facilitate cleavage of the key complement activation-specific protein fragment, C3b, forming iC3b that no longer participates in the complement cascade. We refined a three-dimensional solution structure of recombinant FH1-3 based on nuclear Overhauser effects and RDCs. We then employed a rudimentary series of RDC datasets, collected in media containing magnetically aligned bicelles (disk-like particles formed from phospholipids) under three different conditions, to estimate interdomain motions. This circumvents a requirement of previous approaches for technically difficult collection of five independent RDC datasets. More than 80% of conformers of this predominantly extended three-domain molecule exhibit flexions of < 40 °. Such segmental flexibility (together with the local dynamics of the hypervariable loop within domain 3), could facilitate recognition of C3b via initial anchoring and eventual reorganization of modules to the conformation captured in the previously solved crystal structure of a C3b:FH1-4 complex

PDBe: Protein Data Bank in Europe

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed ‘PDBeView Atlas pages’ provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe’s active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis

Kondo Effect on Mesoscopic Scale (Review)

Following the discovery of the Kondo effect the bulk transport and magnetic behavior of the dilute magnetic alloys have been successfully described. In the last fifteen years new directions have been developed as the study of the systems of reduced dimensions and the artificial atoms so called quantum dots. In this review the first subject is reviewed starting with the scanning tunneling microscope (STM) study of a single magnetic impurity. The next subject is the reduction of the amplitude of the Kondo effect in samples of reduced dimension which was explained by the surface magnetic anisotropy which blocks the motion of the integer spin nearby the surface. The electron dephasing and energy relaxation experiments are discussed with the possible explanation including the surface anisotropy, where the situation in cases of integer and half-integer spins is very different. Finally, the present situation of the theory of dynamical structural defects is briefly presented which may lead to two-channel Kondo behavior.Comment: 8 pages, submitted to the JPSJ Special Issue "Kondo effect -- 40 years after the Discovery

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway

In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding). However, we do not know how PDI distinguishes folded, partly-folded and unfolded protein substrates. As a model intermediate in an oxidative folding pathway, we prepared a two-disulfide mutant of basic pancreatic trypsin inhibitor (BPTI) and showed by NMR that it is partly-folded and highly dynamic. NMR studies show that it binds to PDI at the same site that binds peptide ligands, with rapid binding and dissociation kinetics; surface plasmon resonance shows its interaction with PDI has a Kd of ca. 10−5 M. For comparison, we characterized the interactions of PDI with native BPTI and fully-unfolded BPTI. Interestingly, PDI does bind native BPTI, but binding is quantitatively weaker than with partly-folded and unfolded BPTI. Hence PDI recognizes and binds substrates via permanently or transiently unfolded regions. This is the first study of PDI's interaction with a partly-folded protein, and the first to analyze this folding catalyst's changing interactions with substrates along an oxidative folding pathway. We have identified key features that make PDI an effective catalyst of oxidative protein folding – differential affinity, rapid ligand exchange and conformational flexibility

Sediment structure and physicochemical changes following tidal inundation at a large open coast managed realignment site

Managed realignment (MR) schemes are being implemented to compensate for the loss of intertidal saltmarsh habitats by breaching flood defences and inundating the formerly defended coastal hinterland. However, studies have shown that MR sites have lower biodiversity than anticipated, which has been linked with anoxia and poor drainage resulting from compaction and the collapse of sediment pore space caused by the site's former terrestrial land use. Despite this proposed link between biodiversity and soil structure, the evolution of the sediment sub-surface following site inundation has rarely been examined, particularly over the early stages of the terrestrial to marine or estuarine transition. This paper presents a novel combination of broad- and intensive-scale analysis of the sub-surface evolution of the Medmerry Managed Realignment Site (West Sussex, UK) in the three years following site inundation. Repeated broad-scale sediment physiochemical datasets are analysed to assess the early changes in the sediment subsurface and the preservation of the former terrestrial surface, comparing four locations of different former land uses. Additionally, for two of these locations, high-intensity 3D-computed X-ray microtomography and Itrax micro-X-ray fluorescence spectrometry analyses are presented. Results provide new data on differences in sediment properties and structure related to the former land use, indicating that increased agricultural activity leads to increased compaction and reduced porosity. The presence of anoxic conditions, indicative of poor hydrological connectivity between the terrestrial and post-inundation intertidal sediment facies, was only detected at one site. This site has experienced the highest rate of accretion over the terrestrial surface (ca. 7 cm over 36 months), suggesting that poor drainage is caused by the interaction (or lack of) between sediment facies rather than the former land use. This has significant implications for the design of future MR sites in terms of preparing sites, their anticipated evolution, and the delivery of ecosystem services

Dephasing of Electrons in Mesoscopic Metal Wires

We have extracted the phase coherence time $\tau_{\phi}$ of electronic quasiparticles from the low field magnetoresistance of weakly disordered wires made of silver, copper and gold. In samples fabricated using our purest silver and gold sources, $\tau_{\phi}$ increases as $T^{-2/3}$ when the temperature $T$ is reduced, as predicted by the theory of electron-electron interactions in diffusive wires. In contrast, samples made of a silver source material of lesser purity or of copper exhibit an apparent saturation of $\tau_{\phi}$ starting between 0.1 and 1 K down to our base temperature of 40 mK. By implanting manganese impurities in silver wires, we show that even a minute concentration of magnetic impurities having a small Kondo temperature can lead to a quasi saturation of $\tau_{\phi}$ over a broad temperature range, while the resistance increase expected from the Kondo effect remains hidden by a large background. We also measured the conductance of Aharonov-Bohm rings fabricated using a very pure copper source and found that the amplitude of the $h/e$ conductance oscillations increases strongly with magnetic field. This set of experiments suggests that the frequently observed ``saturation'' of $\tau_{\phi}$ in weakly disordered metallic thin films can be attributed to spin-flip scattering from extremely dilute magnetic impurities, at a level undetectable by other means.Comment: 16 pages, 11 figures, to be published in Physical Review

Barriers to access to opioid medicines:a review of national legislation and regulations of 11 central and eastern European countries

Control measures designed to prevent the misuse of opioid medicines can often unintentionally restrict legitimate medical use, leaving patients with cancer in pain. This study aimed to develop and validate an assessment instrument based on WHO policy guidelines to systematically identify legal and regulatory barriers to opioid access in 11 European countries (Bulgaria, Cyprus, Estonia, Greece, Hungary, Latvia, Lithuania, Serbia, Slovakia, Slovenia, and Turkey) as part of the Access to Opioid Medication in Europe project. Relevant legislation and regulations were independently assessed by three reviewers and potential barriers were identified within nine categories including prescribing, penalties, and others. Potential barriers were identified in all countries, ranging from 22 potential barriers (Cyprus) to 128 potential barriers (Lithuania). The total number of barriers in a single category varied from one (Slovenia, usage category) to 49 (Greece, prescribing category). Differences, such as prescription validity, varied within one category, ranging from 5 days (Hungary) to 13 weeks (Cyprus). The results of this Review should give rise to a national review and revision of provisions that impede access to opioids, disproportionate to their (intended) benefit in preventing misuse, in these 11 European countries

Demonstration of Binding of Neuronal Calcium Sensor-1 to the Ca(v)2.1 P/Q-Type Calcium Channel

[Image: see text] In neurons, entry of extracellular calcium (Ca(2+)) into synaptic terminals through Ca(v)2.1 (P/Q-type) Ca(2+) channels is the driving force for exocytosis of neurotransmitter-containing synaptic vesicles. This class of Ca(2+) channel is, therefore, pivotal during normal neurotransmission in higher organisms. In response to channel opening and Ca(2+) influx, specific Ca(2+)-binding proteins associate with cytoplasmic regulatory domains of the P/Q channel to modulate subsequent channel opening. Channel modulation in this way influences synaptic plasticity with consequences for higher-level processes such as learning and memory acquisition. The ubiquitous Ca(2+)-sensing protein calmodulin (CaM) regulates the activity of all types of mammalian voltage-gated Ca(2+) channels, including the P/Q class, by direct binding to specific regulatory motifs. More recently, experimental evidence has highlighted a role for additional Ca(2+)-binding proteins, particularly of the CaBP and NCS families in the regulation of P/Q channels. NCS-1 is a protein found from yeast to humans and that regulates a diverse number of cellular functions. Physiological and genetic evidence indicates that NCS-1 regulates P/Q channel activity, including calcium-dependent facilitation, although a direct physical association between the proteins has yet to be demonstrated. In this study, we aimed to determine if there is a direct interaction between NCS-1 and the C-terminal cytoplasmic tail of the Ca(v)2.1 α-subunit. Using distinct but complementary approaches, including in vitro binding of bacterially expressed recombinant proteins, fluorescence spectrophotometry, isothermal titration calorimetry, nuclear magnetic resonance, and expression of fluorescently tagged proteins in mammalian cells, we show direct binding and demonstrate that CaM can compete for it. We speculate about how NCS-1/Ca(v)2.1 association might add to the complexity of calcium channel regulation mediated by other known calcium-sensing proteins and how this might help to fine-tune neurotransmission in the mammalian central nervous system