CNR Institute of Crystallography

Roma, Italy

CNR Institute of Crystallography

Roma, Italy
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Loiodice F.,University of Bari | Pochetti G.,CNR Institute of Crystallography
Current Topics in Medicinal Chemistry | Year: 2011

Peroxisome Proliferator-Activated Receptors (PPARs) are ligand-activated transcription factors that govern lipid and glucose homeostasis playing a central role in cardiovascular disease, obesity, and diabetes. These receptors show a high degree of stereoselectivity towards several classes of drugs. This review provides an overview of most papers reporting the influence of stereochemistry on PPAR activation. Some cases in which chirality is a crucial point in determining the PPAR binding mode are reviewed and discussed with the aim to show how enantiomeric recognition originates at the molecular level. The structural characterization by crystallographic methods of complexes formed by PPARs with their ligands turns out to be an essential tool to explain receptor stereoselectivity. © 2011 Bentham Science Publishers Ltd.


News Article | December 13, 2016
Site: www.eurekalert.org

An exciting X-ray imaging technology has been successfully developed to the point where it is now ready for translation into all kinds of beneficial applications, including potentially life-saving uses in security and healthcare. Funded by the Engineering and Physical Sciences Research Council (EPSRC), a major five-year project led by UCL (University College London) has achieved this breakthrough. The work also involved dozens of industrial, academic and research partners in the UK and worldwide. Compared with conventional X-rays, the technology can, for example, identify tumours in living tissue earlier and spot smaller cracks and defects in materials. This is because it excels at determining different shapes and different types of matter - a capability that conventional X-rays could only match by using prohibitively high doses of radiation. The technique at the heart of the advance is called phase-contrast X-ray imaging. Instead of measuring the extent to which tissue or materials absorb radiation - as in conventional X-ray imaging - it measures the physical effect that passing through different types of tissue or material has on the speed of the X-ray itself. Professor Alessandro Olivo, who led the project team, says: "The technique has been around for decades but it's been limited to large-scale synchrotron facilities such as Oxfordshire's Diamond Light Source. We've now advanced this embryonic technology to make it viable for day-to-day use in medicine, security applications, industrial production lines, materials science, non-destructive testing, the archaeology and heritage sector, and a whole range of other fields." This vast potential is already beginning to be explored. For example: Professor Olivo says: "This has the potential to be incredibly versatile, game-changing technology. We're currently negotiating with a number of companies to explore how it could be put to practical use. There's really no limit to the benefits this technique could deliver." For media enquiries contact: Alessandro Olivo, Professor of Applied Physics, UCL, tel: 0207 679 2444, e-mail: a.olivo@ucl.ac.uk; or the EPSRC Press Office, tel: 01793 444 404, e-mail: pressoffice@epsrc.ac.uk The 5-year project Transforming the Use of X-rays in Science and Society ran from November 2011 to October 2016 and received £1.05 million in EPSRC funding under the Challenging Engineering programme. The project created 28 new collaborations and produced around 75 journal papers. Partners and collaborators included: Academia: Imperial College London; Queen Mary University of London; University of Oxford; Ludwig-Maximillian University, Munich; University of Washington in St Louis, Missouri; Kyoto University; Heriot-Watt University; University of Bristol; University of Dundee; University of Glasgow; University of Strathclyde; University of Saskatchewan; University of Trieste; University of Pisa. Research Institutes/Facilities: Diamond Light Source; ELETTRA Sincrotrone Trieste ScpA; European Synchrotron Radiation Facility; Research Complex at Harwell; CNR Institute of Crystallography - Italy; EMPA Switzerland; Barts Health NHS Trust; INFN Istituto Nazionale di Fisica Nucleare, Pisa and Trieste Sections. Within UCL: Department of Mechanical Engineering; Department of Chemical Engineering; Department of Physics and Astronomy; London Centre for Nanotechnology (a joint UCL-Imperial College establishment); Institute of Child Health; Great Ormond Street Hospital. The Engineering and Physical Sciences Research Council (EPSRC): As the main funding agency for engineering and physical sciences research, our vision is for the UK to be the best place in the world to Research, Discover and Innovate. By investing £800 million a year in research and postgraduate training, we are building the knowledge and skills base needed to address the scientific and technological challenges facing the nation. Our portfolio covers a vast range of fields from healthcare technologies to structural engineering, manufacturing to mathematics, advanced materials to chemistry. The research we fund has impact across all sectors. It provides a platform for future economic development in the UK and improvements for everyone's health, lifestyle and culture. We work collectively with our partners and other Research Councils on issues of common concern via Research Councils UK. http://www. UCL (University College London): UCL was founded in 1826. We were the first English university established after Oxford and Cambridge, the first to open up university education to those previously excluded from it, and the first to provide systematic teaching of law, architecture and medicine. We are among the world's top universities, as reflected by performance in a range of international rankings and tables. UCL currently has over 38,000 students from 150 countries and over 12,000 staff. Our annual income is more than £1 billion. Wellcome Trust: Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate.


Rea G.,CNR Institute of Crystallography | Antonacci A.,CNR Institute of Crystallography | Giardi M.T.,CNR Institute of Crystallography
Critical Reviews in Food Science and Nutrition | Year: 2013

In recent years, both food quality and its effect on human health have become a fundamental issue all over the world. As a consequence of this new and increased awareness, American, European, and Asian policymakers have strongly encouraged the research programs on food quality and safety thematic. Attempts to improve human health and to satisfy people's desire for healthcare without intake of pharmaceuticals, has led the food industry to focus attention on functional or nutraceutical food. For a long time, compounds with nutraceutical activity have been produced chemically, but the new demands for a sustainable life have gradually led the food industry to move towards natural compounds, mainly those derived from plants. Many phytochemicals are known to promote good health, but, sometimes, undesirable effects are also reported. Furthermore, several products present on the market show few benefits and sometimes even the reverse - unhealthy effects; the evidence of efficacy is often unconvincing and epidemiological studies are necessary to prove the truth of their claims. Therefore, there is a need for reliable analytical control systems to measure the bioactivity, content, and quality of these additives in the complex food matrix. This review describes the most widespread nutraceutics and an analytical control of the same using recently developed biosensors which are promising candidates for routine control of functional foods. © 2013 Copyright Taylor and Francis Group, LLC.


Giacovazzo C.,CNR Institute of Crystallography
Acta Crystallographica Section A: Foundations and Advances | Year: 2015

For a given unknown crystal structure (the target), n random structures, arbitrarily designed without any care for their chemical consistency and usually uncorrelated with the target, are sheltered in the same unit cell as the target structure and submitted to the same space-group symmetry. (These are called ancil structures.) The composite structures, whose electron densities are the sum of the target and of the ancil electron densities, are denoted derivatives. No observed diffraction amplitudes are available for them: in order to emphasize their unreal nature, the term phantom is added. The paper describes the theoretical basis by which the phantom derivative method may be used to phase the target structure. It may be guessed that 100-300 ancil structures may be sufficient for phasing a target structure, so that the phasing technique may be denoted as the multiple phantom derivative method. Ancil phases and amplitudes may be initially combined with observed target magnitudes to estimate amplitudes and phases of the corresponding phantom derivative. From them suitable algorithms allow one to obtain poor target phase estimates, which are often improved by combining the indications arising from each derivative. Probabilistic criteria are described to recognize the most reliable target phase estimates. The method is cyclic: the target phase estimates just obtained are used to improve amplitudes and phases of each derivative, which, in their turn, are employed to provide better target phase estimates. The method is a fully ab initio method, because it needs only the experimental data of the target structure. The term derivative is maintained with reference to SIR-MIR (single isomorphous replacement-multiple isomorphous replacement) techniques, even if its meaning is different: therefore the reader should think of the phantom derivative method more as a new method than as a variant of SIR-MIR techniques. The differences are much greater than the analogies. The paper also describes how phantom derivatives may be used for improving structure models obtained via other ab initio or non-ab initio techniques. The method is expected to be insensitive to the structural complexity of the target and to the target experimental data resolution, provided it is better than 4-6 Å. © 2015 International Union of Crystallograph.


Scognamiglio V.,CNR Institute of Crystallography
Biosensors and Bioelectronics | Year: 2013

In the last decades, a wide multitude of research activity has been focused on the development of biosensors for glucose monitoring, devoted to overcome the challenges associated with smart analytical performances with commercial implications. Crucial issues still nowadays elude biosensors to enter the market, such as sensitivity, stability, miniaturisation, continuous and in situ monitoring in a complex matrix. A noteworthy tendency of biosensor technology is likely to push towards nanotechnology, which allows to reduce dimensions at the nanoscale, consenting the construction of arrays for high throughput analysis with the integration of microfluidics, and enhancing the performance of the biological components by using new nanomaterials. This review aims to highlight current trends in biosensors for glucose monitoring based on nanotechnology, reporting widespread representative examples of the recent approaches for nanobiosensors over the past 10 years. Progress in nanotechnology for the development of biosensing systems for blood glucose level monitoring will be discussed, in view of their design and construction on the bases of the new materials offered by nanotechnology. © 2013 Elsevier B.V.


Carrozzini B.,CNR Institute of Crystallography | Cascarano G.L.,CNR Institute of Crystallography | Comunale G.,University of Basilicata | Giacovazzo C.,CNR Institute of Crystallography | Mazzone A.,CNR Institute of Crystallography
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

VLD (vive la difference) is a novel ab initio phasing approach that is able to drive random phases to the correct values. It has been applied to small, medium and protein structures provided that the data resolution was atomic. It has never been used for non-ab initio cases in which some phase information is available but the data resolution is usually very far from 1 14;Å. In this paper, the potential of VLD is tested for the first time for a classical non-ab initio problem: molecular replacement. Good preliminary experimental results encouraged the construction of a pipeline for leading partial molecular-replacement models with errors to refined solutions in a fully automated way. The pipeline moduli and their interaction are described, together with applications to a wide set of test cases. © 2013 International Union of Crystallography.


Caliandro R.,CNR Institute of Crystallography | Carrozzini B.,CNR Institute of Crystallography | Cascarano G.L.,CNR Institute of Crystallography | Comunale G.,University of Basilicata | And 2 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2014

Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (C map), the VLD (vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and the free lunch extrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use of ARP/wARP to check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures: e.g. the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version of SIR2014. © 2014 International Union of Crystallography.


Li H.,Italian Institute of Technology | Zanella M.,Italian Institute of Technology | Genovese A.,Italian Institute of Technology | Povia M.,Italian Institute of Technology | And 3 more authors.
Nano Letters | Year: 2011

We demonstrate that it is possible to convert CdSe nanocrystals of a given size, shape (either spherical or rod shaped), and crystal structure (either hexagonal wurtzite, i.e., hexagonal close packed (hcp), or cubic sphalerite, i.e., face-centered cubic (fcc)), into ZnSe nanocrystals that preserve all these characteristics of the starting particles (i.e., size, shape, and crystal structure), via a sequence of two cation exchange reactions, namely, Cd 2+ →Cu+ →Zn2+. When starting from hexagonal wurtzite CdSe nanocrystals, the exchange of Cd2+ with Cu+ yields Cu2Se nanocrystals in a metastable hexagonal phase, of which we could follow the transformation to the more stable fcc phase for a single nanorod, under the electron microscope. Remarkably, these metastable hcp Cu2Se nanocrystals can be converted in solution into ZnSe nanocrystals, which yields ZnSe nanocrystals in a pure hcp phase. © 2011 American Chemical Society.


Giacovazzo C.,CNR Institute of Crystallography
Acta Crystallographica Section A: Foundations of Crystallography | Year: 2015

Crystallographic least squares are a fundamental tool for crystal structure analysis. In this paper their properties are derived from functions estimating the degree of similarity between two electron-density maps. The new approach leads also to modifications of the standard least-squares procedures, potentially able to improve their efficiency. The role of the scaling factor between observed and model amplitudes is analysed: the concept of unlocated model is discussed and its scattering contribution is combined with that arising from the located model. Also, the possible use of an ancillary parameter, to be associated with the classical weight related to the variance of the observed amplitudes, is studied. The crystallographic discrepancy factors, basic tools often combined with least-squares procedures in phasing approaches, are analysed. The mathematical approach here described includes, as a special case, the so-called vector refinement, used when accurate estimates of the target phases are available. © 2015 International Union of Crystallography.


Carrozzini B.,CNR Institute of Crystallography | Cascarano G.L.,CNR Institute of Crystallography | Giacovazzo C.,CNR Institute of Crystallography | Mazzone A.,CNR Institute of Crystallography
Acta Crystallographica Section D: Biological Crystallography | Year: 2015

The REVAN pipeline aiming at the solution of protein structures via molecular replacement (MR) has been assembled. It is the successor to REVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. The REVAN and REVA procedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases, REVAN combines a variety of programs and algorithms (REMO09, REFMAC, DM, DSR, VLD, free lunch, Coot, Buccaneer and phenix.autobuild). The MR model, suitably rotated and positioned, is first refined by a standard REFMAC refinement procedure, and the corresponding electron density is then submitted to cycles of DM-VLD-REFMAC. The next REFMAC applications exploit the better electron densities obtained at the end of the VLD-EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in which Coot plays a basic role, and it is then cyclically resubmitted to REFMAC-EDM-VLD cycles. The phases thus obtained are submitted to free lunch and allow most of the test structures studied by DiMaio et al. [(2011), Nature (London), 473, 540-543] to be solved without using energy-guided programs. © 2015 International Union of Crystallography.

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