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In this paper, we present several study cases focused on marine, oceanographic, and atmospheric environments, which would greatly benefit from the use of a deployable system for small satellite observations. As opposed to the large standard ones, small satellites have become an effective and affordable alternative access to space, owing to their lower costs, innovative design and technology, and higher revisiting times, when launched in a constellation configuration. One of the biggest challenges is created by the small satellite instrumentation working in the visible (VIS), infrared (IR), and microwave (MW) spectral ranges, for which the resolution of the acquired data depends on the physical dimension of the telescope and the antenna collecting the signal. In this respect, a deployable payload, fitting the limited size and mass imposed by the small satellite architecture, once unfolded in space, can reach performances similar to those of larger satellites. In this study, we show how ecology and Earth Observations can benefit from data acquired by small satellites, and how they can be further improved thanks to deployable payloads. We focus on DORA—Deployable Optics for Remote sensing Applications—in the VIS to TIR spectral range, and on a planned application in the MW spectral range, and we carry out a radiometric analysis to verify its performances for Earth Observation studies. [ABSTRACT FROM AUTHOR]

The dynamics of irregularly shaped particles subjected to the combined effect of gas drag and radiative forces and torques in a cometary environment is investigated. The equations of motion are integrated over distances from the nucleus surface up to distances where the gas drag is negligible. The aerodynamic forces and torques are computed assuming a spherically symmetric expanding gas. The calculations are limited to particle sizes in the geometric optics limit, which is the range of validity of our radiative torque calculations. The dynamical behaviour of irregular particles is quite different to those exhibited by non-spherical but symmetric particles such as spheroids. An application of the dynamical model to comet 67P/Churyumov–Gerasimenko, the target of the Rosetta mission, is made. We found that, for particle sizes larger than ∼10 μm, the radiative torques are negligible in comparison with the gas-driven torques up to a distance of ∼100 km from the nucleus surface. The rotation frequencies of the particles depend on their size, shape, and the heliocentric distance, while the terminal velocities, being also dependent on size and heliocentric distance, show only a very weak dependence on particle shape. The ratio of the sum of the particles projected areas in the sun-to-comet direction to that of the sum of the particles projected areas in any direction perpendicular to it is nearly unity, indicating that the interpretation of the observed u-shaped scattering phase function by Rosetta /OSIRIS on comet 67P coma cannot be linked to mechanical alignment of the particles. [ABSTRACT FROM AUTHOR]

Studies nuclear spin relaxation for an S=1 system and its field dependence in the presence of zero-field splitting. Electron spin energy level structure; Causes of the electron spin relaxation; Spectral densities; Nuclear magnetic relaxation dispersion profiles.

Landslides have been identified on several solar system bodies, and different mechanisms have been proposed to explain their runout length. We analyze images from the Rosetta mission and report the global characterization of such features on comet 67P/Churyumov‐Gerasimenko's surface. By assuming the height to runout length as an approximation for the friction coefficient of landslide material, we find that on comet 67P, this ratio falls between 0.50 and 0.97. Such unexpected high values reveal a rocky‐type mechanical behavior that is much more akin to Earth dry landslides than to icy satellites' mass movements. This behavior indicates that 67P and likely comets in general are characterized by consolidated materials possibly rejecting the idea that they are fluffy aggregates. The variability of the runout length among 67P landslides can be attributed to the different volatile content located in the top few meters of the cometary crust, which can drive the mass movement. Plain Language Summary: Comet 67P Churyumov‐Gerasimenko has been imaged with unprecedented spatial detail thanks to the high‐resolution OSIRIS camera (Optical, Spectroscopic and Infrared Remote Imaging System) on board the Rosetta spacecraft. 67P is characterized by an extremely diverse morphology comprising different surface features such as rough consolidated terrains, smooth plains, unconsolidated mantles, pits, fractures, cliffs, cuestas, ubiquitous boulders, and layers. The peculiarity of 67P is also reflected by the widespread presence of landslides. By using high‐resolution images, we analyze the shape and aspect ratio of the landslides located on comet 67P finding a mechanical behavior of the cometary material that is more akin to Earth dry landslides than to icy satellites' mass movements. These results make 67P a very peculiar object, mainly composed by ices and refractory materials but characterized by rocky‐type properties rather than icy‐type characteristics. In addition, the considerable variability among the different landslides of 67P suggests that different volatile contents located in the top few meters of the cometary crust play a fundamental role on mass movement, hence being a general indicator for the subsurface cometary heterogeneities. Key Points: The height to runout length (H/L) of comet 67P/Churyumov‐Gerasimenko landslides ranges between 0.50 and 0.9767P landslide reveal a rocky‐type mechanical behavior indicating that comets are made by consolidated materialsThe H/L variability is an indicator of the different volatile content located in the top few meters of the cometary crust [ABSTRACT FROM AUTHOR]

This contribution deals with two different hypotheses on the origin of superficial water on the Earth: the Endogenous hypothesis and the Exogenous one. They proposed that water either was brought to the surface of the Earth from the deep interior of the Earth or would have come to the Earth from celestial bodies that bombarded the planet billions of years ago. The evidence from recent astronomical and geological findings supporting the two alternative hypotheses will be discussed. [ABSTRACT FROM AUTHOR]

Summary: The paper reviews properties of comets, from historical sightings and interpretations, to contemporary ground- and space-based knowledge. The importance of comets in understanding the present Solar System and its dynamical, physical and chemical evolution, their relationship with other minor bodies, their possible role for the very early phases of our Earth, will be examined. Emphasis will be on the results of the recently completed European Rosetta mission to comet 67P/Churyumov-Gerasimenko, in particular those by OSIRIS, its imaging system. It is fair to say that Rosetta's results represent a most important step in the development of cometary science, whose full implications start just to surface and will be fully appreciated over several more years. [ABSTRACT FROM AUTHOR]

Pits have been observed on many cometary nuclei mapped by spacecraft. It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments and models cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts. Alternative mechanisms like explosive activity have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface. [ABSTRACT FROM AUTHOR]

Pre-analytical treatments of bacteria are crucial steps in bacterial metabolomics studies. In order to achieve reliable samples that can best represent the global metabolic profile in vivo both qualitatively and quantitatively, many sample treatment procedures have been developed. The use of different methods makes it difficult to compare the results among different groups. In this work, E. coli samples were tested by using NMR spectroscopy. Both liquid N and cold methanol quenching procedures reduce the cell membrane integrity and cause metabolites leakage. However, liquid N quenching affected the cell viability and the NMR metabolites' profile less than cold methanol procedure. Samples obtained by metabolite extraction were significantly superior over cell suspensions and cell lysates, with a higher number of detectable metabolites. Methanol/chloroform extraction proved most efficient at extraction of intracellular metabolites from both qualitative and quantitative points of view. Finally, standard operating procedures of bacterial sample treatments for NMR metabolomics study are presented. [ABSTRACT FROM AUTHOR]

Spirometry is used to establish the diagnosis of chronic obstructive pulmonary disease (COPD) and to assess disease progression, but it seems inadequate to characterize COPD phenotypes. Metabolomics has been introduced for molecular fingerprinting of biosamples in a variety of clinical disorders. The aim of the study was to establish whether exhaled breath condensate (EBC) in COPD features a distinct metabolic fingerprint, and to identify the metabolites that characterize the EBC profile in COPD. EBC was collected using a home-made glass condenser in 37 stable COPD patients, and 25 non-obstructed controls. Samples were analyzed using proton nuclear magnetic resonance spectroscopy (H NMR). Random forest was applied for both supervised and unsupervised learning, using spectral buckets as input variables. Metabolomics of EBC discriminated COPD patients from controls with an overall accuracy of 86 %. As compared to controls, EBC from COPD featured significantly lower ( p < 0.05) levels of acetone, valine and lysine, and significantly higher ( p < 0.05) levels of lactate, acetate, propionate, serine, proline, and tyrosine. Based on unsupervised analysis of NMR spectra, the COPD sample was split in three clusters, one of which had the highest prevalence of radiologic emphysema. NMR spectroscopy of EBC holds promise in COPD fingerprinting. It may prove valuable in outcome studies, and in assessing the efficacy of therapeutic interventions. [ABSTRACT FROM AUTHOR]

Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins–NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin–form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins. The Ndor1-anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells. [ABSTRACT FROM AUTHOR]

Triplex als Alternative: Metadynamikrechnungen deuten darauf hin, dass das Thrombin bindende Aptamer (TBA) neben dem üblichen G ‐ Quadruplex auch eine stabile G ‐ Triplex ‐ Struktur einnehmen kann (siehe Schema; rote Kugel: K+ ‐ Ion). Ein 11 ‐ mer ‐ Oligonucleotid bildet ebenfalls einen stabilen G ‐ Triplex, dessen Struktur und thermodynamische Eigenschaften charakterisiert wurden. [ABSTRACT FROM AUTHOR]

Triplex with a twist: Through metadynamics calculations, the thrombin binding aptamer (TBA) has been shown to adopt a stable G‐triplex structural motif, in addition to the usual G‐quadruplex (see scheme). An 11‐mer oligonucleotide was also shown to form a stable G‐triplex, whose structural and thermodynamic properties have been characterized. [ABSTRACT FROM AUTHOR]

Human S100A14 is a member of the EF-hand calcium-binding protein family that has only recently been described in terms of its functional and pathological properties. The protein is overexpressed in a variety of tumor cells and it has been shown to trigger receptor for advanced glycation end products (RAGE)-dependent signaling in cell cultures. The solution structure of homodimeric S100A14 in the apo state has been solved at physiological temperature. It is shown that the protein does not bind calcium(II) ions and exhibits a 'semi-open' conformation that thus represents the physiological structure of the S100A14. The lack of two ligands in the canonical EF-hand calcium(II)-binding site explains the negligible affinity for calcium(II) in solution, and the exposed cysteines and histidine account for the observed precipitation in the presence of zinc(II) or copper(II) ions. [ABSTRACT FROM AUTHOR]

The WeNMR () project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI). [ABSTRACT FROM AUTHOR]

Metabolomics is a science that provides a dynamic portrait of the metabolic status of a biological system. Down from genomics, transcriptomics, and proteomics, metabolomics assesses end product metabolites and small intermediate molecules. In oncology, identification and quantification of metabolites and correlation with critical metabolic pathways in carcinogenesis may provide insight into tumoral biology. In breast cancer, promising early work suggests that metabolomics might enhance current clinical practice by refining biological subclassification, improving prediction of recurrence, and aiding in treatment decisions. [ABSTRACT FROM AUTHOR]

We have recently proposed sedimented solute NMR (SedNMR) as a solid-state method to access biomolecules without the need of crystallization or other sample manipulation. The drawback of SedNMR is that samples are intrinsically diluted and this is detrimental for the signal intensity. Ultracentrifugal devices can be used to increase the amount of sample inside the rotor, overcoming the intrinsic sensitivity limitation of the method. We designed two different devices and we here report the directions for using such devices and the relevant equations for determining the parameters for sedimentation. [ABSTRACT FROM AUTHOR]

Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis. As a result of increases in the prevalences of obesity, insulin resistance, and hyperlipidemia, the number of people with hepatic steatosis continues to increase. Differences in susceptibility to steatohepatitis and its progression to cirrhosis have been attributed to a complex interplay of genetic and external factors all addressing the intracellular network. Increase in sugar or refined carbohydrate consumption results in an increase of insulin and insulin resistance that can lead to the accumulation of fat in the liver. Here we demonstrate how a multidisciplinary approach encompassing cellular reprogramming, transcriptomics, proteomics, metabolomics, modeling, network reconstruction, and data management can be employed to unveil the mechanisms underlying the progression of steatosis. Proteomics revealed reduced AKT/mTOR signaling in fibroblasts derived from steatosis patients and further establishes that the insulin-resistant phenotype is present not only in insulin-metabolizing central organs, e.g., the liver, but is also manifested in skin fibroblasts.Transcriptome data enabled the generation of a regulatory network based on the transcription factor SREBF1, linked to a metabolic network of glycerolipid, and fatty acid biosynthesis including the downstream transcriptional targets of SREBF1 which include LIPIN1 (LPIN) and low density lipoprotein receptor. Glutathione metabolism was among the pathways enriched in steatosis patients in comparison to healthy controls. By using a model of the glutathione pathway we predict a significant increase in the flux through glutathione synthesis as both gamma-glutamylcysteine synthetase and glutathione synthetase have an increased flux.We anticipate that a larger cohort of patients and matched controls will confirm our preliminary findings presented here. [ABSTRACT FROM AUTHOR]

Copper chaperone for superoxide dismutase 1 (SOD1), CCS, is the physiological partner for the complex mechanism of SOD1 maturation. We report an in vitro model for human CCS-dependent SOD1 maturation based on the study of the interactions of human SOD1 (hSODl) with full-length WT human CCS (hCCS), as well as with hCCS mutants and various truncated constructs comprising one or two of the protein's three domains. The synergy between electrospray ionization mass spectrometry (ESI-MS) and NMR is fully exploited. This is an in vitro study of this process at the molecular level. Domain 1 of hCCS is necessary to load hSODl with Cu(l), requiring the heterodimeric complex formation with hSODl fostered by the interaction with domain 2. Domain 3 is responsible for the catalytic formation of the hSODl Cys-57-Cys-146 disulfide bond, which involves both hCCS Cys-244 and Cys-246 via disulfide transfer. [ABSTRACT FROM AUTHOR]

Abstract: Background: Metabolomics, a global study of metabolites and small molecules, is a novel expanding field. In this pilot study, metabolomics has been applied to serum samples from women with metastatic breast cancer to explore outcomes and response to treatment. Patients and methods: Pre-treatment and serial on-treatment serum samples were available from an international clinical trial in which 579 women with metastatic breast cancer were randomized to paclitaxel plus either a targeted anti-HER2 treatment (lapatinib) or placebo. Serum metabolomic profiles were obtained using 600 MHz nuclear magnetic resonance spectroscopy. Profiles were compared with time to progression, overall survival and treatment toxicity. Results: Pre- and on-treatment serum samples were assessed for over 500 patients. Unbiased metabolomic profiles in the biologically unselected overall trial population did not correlate with outcome or toxicity. In a subgroup of patients with HER2-positive disease treated with paclitaxel plus lapatinib, metabolomic profiles from patients in the upper and lower thirds of the dataset showed significant differences for time to progression (N = 22, predictive accuracy = 89.6%) and overall survival (N = 16, predictive accuracy = 78.0%). Conclusions: In metastatic breast cancer, metabolomics may play a role in sub selecting patients with HER2 positive disease with greater sensitivity to paclitaxel plus lapatinib. [Copyright &y& Elsevier]

The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at . It can be used freely upon registration to the grid with a digital certificate. [ABSTRACT FROM AUTHOR]

The characterization of intrinsically disordered proteins (IDPs) by NMR spectroscopy is made difficult by the extensive spectral overlaps. To overcome the intrinsic low-resolution of the spectra the introduction of high-dimensionality experiments is essential. We present here a set of high-resolution experiments based on direct C-detection which proved useful in the assignment of α-synuclein, a paradigmatic IDP. In particular, we describe the implementation of 4D HCBCACON, HCCCON, HCBCANCO, 4/5D HNCACON and HNCANCO and 3/4D HCANCACO experiments, specifically tailored for spin system identification and backbone resonances sequential assignment. The use of non-uniform-sampling in the indirect dimension and of the H-flip approach to achieve longitudinal relaxation enhancement rendered the experiments very practical. [ABSTRACT FROM AUTHOR]

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ¡on available either in Cu (diamagnetic) or Cu2 (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to 1H-1H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a Gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable. [ABSTRACT FROM AUTHOR]

Abstract: Pseudocontact shifts (pcs) and paramagnetic residual dipolar couplings (rdc) provide structural information that can be used to assess the adequacy of a crystallographic structure to represent the solution structure of a protein. This can be done by attaching a lanthanide binding tag to the protein. There are cases in which only local rearrangements are sufficient to match the NMR data and cases where significant secondary structure or domain rearrangements from the solid state to the solution state are needed. We show that the two cases are easily distinguishable. Whereas the use of solution restraints in the latter case is described in the literature, here we deal with how to obtain a better model of the solution structure in a case (the catalytic domain of the matrix metalloproteinase MMP-1) of the former class. [Copyright &y& Elsevier]

Copper metallochaperones supply copper to cupro-proteins through copper-mediated protein-protein-interactions and it has been hypothesized that metallochaperones thereby inhibit copper from causing damage en route. Evidence is presented in support of this latter role for cyanobacterial metallochaperone, Atx1. In cyanobacteria Atx1 contributes towards the supply of copper to plastocyanin inside thylakoids but it is shown here that in copperreplete medium, copper can reach plastocyanin without Atx1. Unlike metallochaperone-independent copper-supply to superoxide dismutase in eukaryotes, glutathione is not essential for Atxlindependent supply to plastocyanin: Double mutants missing atxl and gshB (encoding glutathione synthetase) accumulate the same number of atoms of copper per cell in the plastocyanin pool as wild type. Critically, Δatx1ΔgshB are hypersensitive to elevated copper relative to wild type cells and also relative to ΔgshB single mutants with evidence that hypersensitivity arises due to the mislocation of copper to sites for other metals including iron and zinc. The zinc site on the amino-terminal domain (ZiaAN) of the P1-type zinctransporting ATPase is especially similar to the copper site of the Atx1 target PacSN, and ZiaAN will bind Cu(l) more tightly than zinc. An NMR model of a substituted-ZiaAN-Cu(l)-Atx1 heterodimer has been generated making it possible to visualize a juxtaposition of residues surrounding the ZiaAN zinc site, including Asp18, which normally repulse Atx1. Equivalent repulsion between bacterial copper metallochaperones and the amino-terminal regions of P1 -type ATPases for metals other than Cu(l) is conserved, again consistent with a role for copper metallochaperones to withhold copper from binding sites for other metals. [ABSTRACT FROM AUTHOR]

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design. [ABSTRACT FROM AUTHOR]

Motivation: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20–40 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols.Results: We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER-based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of three different proteins are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein–ligand adducts.Availability and Implementation: AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http://py-enmr.cerm.unifi.it/access/index/amps-nmr; its use requires registration with a digital certificate.Contact: ivanobertini@cerm.unifi.itSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

In-cell NMR allows characterizing the folding state of a protein as well as posttranslational events at molecular level, in the cellular context. Here, the initial maturation steps of human copper, zinc superoxide dismutase 1 are characterized in the E. coli cytoplasm by in-cell NMR: from the apo protein, which is partially unfolded, to the zinc binding which causes its final quaternary structure. The protein selectively binds only one zinc ion, whereas in vitro also the copper site binds a nonphysiological zinc ion. However, no intramolecular disulfide bridge formation occurs, nor copper uptake, suggesting the need of a specific chaperone for those purposes [ABSTRACT FROM AUTHOR]

Sco proteins are present in all types of organisms, including the vast majority of eukaryotes and many prokaryotes. It is well established that Sco proteins in eukaryotes are involved in the assembly of the Cu cofactor of mitochondrial cytochrome c oxidase; however their precise role in this process has not yet been elucidated at the molecular level. In particular, some but not all eukaryotes including humans possess two Sco proteins whose individual functions remain unclear. There is evidence that eukaryotic Sco proteins are also implicated in other cellular processes such as redox signalling and regulation of copper homeostasis. The range of physiological functions of Sco proteins appears to be even wider in prokaryotes, where Sco-encoding genes have been duplicated many times during evolution. While some prokaryotic Sco proteins are required for the biosynthesis of cytochrome c oxidase, others are most likely to take part in different processes such as copper delivery to other enzymes and protection against oxidative stress. The detailed understanding of the multiplicity of roles ascribed to Sco proteins requires the identification of the subtle determinants that modulate the two properties central to their known and potential functions, i.e. copper binding and redox properties. In this review, we provide a comprehensive summary of the current knowledge on Sco proteins gained by genetic, structural and functional studies on both eukaryotic and prokaryotic homologues, and propose some hints to unveil the elusive molecular mechanisms underlying their functions. This review provides a comprehensive summary of the current knowledge on Sco proteins gained by genetic, structural and functional studies on both eukaryotic and prokaryotic homologues. Hints are given to identify the subtle determinants that modulate the copper binding and the redox properties of Sco proteins, and thus unveil the elusive molecular mechanisms underlying their cellular functions. [ABSTRACT FROM AUTHOR]

Relatively large proteins in solution, spun in NMR rotors for solid samples at typical ultracentrifugation speeds, sediment at the rotor wall. The sedimented proteins provide high-quality solid-state-like NMR spectra suitable for structural investigation. The proteins fully revert to the native solution state when spinning is stopped, allowing one to study them in both conditions. Transiently sedimented proteins can be considered a novel phase as far as NMR is concerned. NMR of transiently sedimented molecules under fast magic angle spinning has the advantage of overcoming protein size limitations of solution NMR without the need of sample crystallization/precipitation required by solid-state NMR. [ABSTRACT FROM AUTHOR]

A structural model of the adduct between human cytochrome c and the human anti-apoptotic protein Bcl-xL, which defines the protein-protein interaction surface, was obtained from solution NMR chemical shift perturbation data. The atomic level information reveals key intermolecular contacts identifying new potentially druggable areas on cytochrome c and Bcl-xL. Involvement of residues on cytochrome c other than those in its complexes with electron transfer partners is apparent. Key differences in the contact area also exist between the Bcl-xL adduct with the Bak peptide and that with cytochrome c. The present model provides insights to the mechanism by which cytochrome c translocated to cytosol can be intercepted, so that the apoptosome is not assembled. [ABSTRACT FROM AUTHOR]

Oxidative protein folding in the mitochondrial intermembrane space requires the transfer of a disulfide bond from MIA40 to the substrate. During this process MIA40 is reduced and regenerated to a functional state through the interaction with the flavin-dependent sulfhydryl oxidase ALR. Here we present the mechanistic basis of ALR-MIA40 interaction at atomic resolution by biochemical and structural analyses of the mitochondrial ALR isoform and its covalent mixed disulfide intermediate with MIA40. This ALR isoform contains a folded FAD-binding domain at the C-terminus and an unstructured, flexible N-terminal domain, weakly and transiently interacting one with the other. A specific region of the N-terminal domain guides the interaction with the MIA40 substrate binding cleft (mimicking the interaction of the substrate itself), without being involved in the import of ALR. The hydrophobicity-driven binding of this region ensures precise protein-protein recognition needed for an efficient electron transfer process. [ABSTRACT FROM AUTHOR]

Sco proteins are widespread in eukaryotic and in many prokaryotic organisms. They have a thioredoxin-like fold and bind a single copper(I) or copper(II) ion through a CXXXC motif and a conserved His ligand, with both tight and weak affinities. They have been implicated in the assembly of the Cu site of cytochrome c oxidase as copper chaperones and/or thioredoxins. In this work we have structurally characterized a Sco domain which is naturally fused with a typical electron transfer molecule, i.e., cytochrome c, in Pseudomonas putida. The thioredoxin-like Sco domain does not bind copper(II), binds copper(I) with weak affinity without involving the conserved His, and has redox properties consisting of a thioredoxin activity and of the ability of reducing copper(II) to copper(I), and iron(III) to iron(II) of the cytochrome c domain. These findings indicate that the His ligand coordination is the discriminating factor for introducing a metallochaperone function in a thioredoxin-like fold, typically responsible for electron transfer processes. A comparative structural analysis of the Sco domain from P. putida versus eukaryotic Sco proteins revealed structural determinants affecting the formation of a tight-affinity versus a weak-affinity copper binding site in Sco proteins. [ABSTRACT FROM AUTHOR]

H NMR metabolic profiling of urine, serum and plasma has been used to monitor the impact of the pre-analytical steps on the sample quality and stability in order to propose standard operating procedures (SOPs) for deposition in biobanks. We analyzed the quality of serum and plasma samples as a function of the elapsed time ( t = 0−4 h) between blood collection and processing and of the time from processing to freezing (up to 24 h). The stability of the urine metabolic profile over time (up to 24 h) at various storage temperatures was monitored as a function of the different pre-analytical treatments like pre-storage centrifugation, filtration, and addition of the bacteriostatic preservative sodium azide. Appreciable changes in the profiles, reflecting changes in the concentration of a number of metabolites, were detected and discussed in terms of chemical and enzymatic reactions for both blood and urine samples. Appropriate procedures for blood derivatives collection and urine preservation/storage that allow maintaining as much as possible the original metabolic profile of the fresh samples emerge, and are proposed as SOPs for biobanking. [ABSTRACT FROM AUTHOR]

The homodimeric structure of human S100A16 in the apo state has been obtained both in the solid state and in solution, resulting in good agreement between the structures with the exception of two loop regions. The homodimeric solution structure of human S100A16 was also calculated in the calcium(II)-bound form. Differently from most S100 proteins, the conformational rearrangement upon calcium binding is minor. This characteristic is likely to be related to the weak binding affinity of the protein for the calcium(II) ions. In turn, this is ascribed to the lack of the glutamate residue at the end of the S100-specific N-domain binding site, which in most S100 proteins provides two important side chain oxygen atoms as calcium(II) ligands. Furthermore, the presence of hydrophobic interactions stronger than for other S100 proteins, present in the closed form of S100A16 between the third and fourth helices, likely make the closed structure of the second EF-hand particularly stable, so even upon calcium(II) binding such a conformation is not disrupted. [ABSTRACT FROM AUTHOR]

We obtained an extended functional annotation of zinc proteins using a combination of bioinformatic methods. This work was performed using a number of available predicted zinc proteomes of various representative organisms, leading to the almost complete annotation of, among others, the predicted human zinc proteome. The computational tools exploited included sequence-based and, when possible, structure-based functional predictions. We assigned a hypothetical function to 74% of the 1,472 sequences analyzed that lacked annotation in the starting dataset. We also added new functional categories, not described in the reference dataset, such as ubiquitin binding and DNA replication. As a general conclusion, we can state that the quality of each functional prediction parallels the amount of information for the sequence analyzed: the larger the amount of information, the more detailed and reliable is the proposed functional prediction. Among the findings, we have propose a zinc binding site for archaeal zinc-importing proteins. Furthermore, we propose two groups of transcriptional regulators that are involved in fatty acid metabolism. [ABSTRACT FROM AUTHOR]

Copper is an essential but potentially harmful trace element required in many enzymatic processes involving redox chemistry. Cellular copper homeostasis in mammals is predominantly maintained by regulating copper transport through the copper import CTR proteins and the copper exporters ATP7A and ATP7B. Once copper is imported into the cell, several pathways involving a number of copper proteins are responsible for trafficking it specifically where it is required for cellular life, thus avoiding the release of harmful free copper ions. In this study we review recent progress made in understanding the molecular mechanisms of copper transport in cells by analyzing structural features of copper proteins, their mode of interaction, and their thermodynamic and kinetic parameters, thus contributing to systems biology of copper within the cell. [ABSTRACT FROM AUTHOR]

Copper is an essential trace element for eukaryotes and most prokaryotes. However, intracellular free copper must be strictly limited because of its toxic side effects. Complex systems for copper trafficking evolved to satisfy cellular requirements while minimizing toxicity. The factors driving the copper transfer between protein partners along cellular copper routes are, however, not fully rationalized. Until now, inconsistent, scattered and incomparable data on the copper-binding affinities of copper proteins have been reported. Here we determine, through a unified electrospray ionization mass spectrometry (ESI-MS)-based strategy, in an environment that mimics the cellular redox milieu, the apparent Cu(I)-binding affinities for a representative set of intracellular copper proteins involved in enzymatic redox catalysis, in copper trafficking to and within various cellular compartments, and in copper storage. The resulting thermodynamic data show that copper is drawn to the enzymes that require it by passing from one copper protein site to another, exploiting gradients of increasing copper-binding affinity. This result complements the finding that fast copper-transfer pathways require metal-mediated protein–protein interactions and therefore protein–protein specific recognition. Together with Cu,Zn-SOD1, metallothioneins have the highest affinity for copper(I), and may play special roles in the regulation of cellular copper distribution; however, for kinetic reasons they cannot demetallate copper enzymes. Our study provides the thermodynamic basis for the kinetic processes that lead to the distribution of cellular copper. [ABSTRACT FROM AUTHOR]