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Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2010.2.3.3-2 | Award Amount: 21.90M | Year: 2010

RNA virus infections kill millions of humans annually, largely due to the lack of suitable vaccines and drugs to control them. This problem is addressed in this FP7 call and in response a consortium of Europes and Asias leading molecular virologists, structural biologists, medicinal chemists and bioinformaticians has been brought together to generate a state-of-the-art drug discovery and design programme. The project aims to identify Small molecule Inhibitor Leads Versus Emerging and neglected RNA viruses (SILVER). It will focus its activities on selected medically important RNA viruses for which the development of drugs is considered essential (Dengue-, entero- and paramyxoviruses), whereas other relatively neglected and/or emerging RNA viruses will be explored to identify the most promising viral protein targets and antiviral compounds. A pipeline strategy has been developed to enable the inclusion in SILVER of viruses at all levels of existing knowledge. Targets for potential drugs include infectious virus, structurally characterised viral enzymes and other proteins. Leads for currently available antiviral drugs have been identified by screening compound libraries in virus-infected cell culture systems and in vitro assays using purified viral enzymes. Selective inhibitors of viral replication have also been (and are being) derived using detailed structural knowledge of viral proteins and structure-based drug design. Hits will be assayed using individual viral protein targets and replicative proteins in complex with viral RNA. The potential protective activity of the most potent inhibitors, that have a favourable (in vitro) ADME-tox profile, will be assessed in relevant infection models in animals. Licenses on promising compounds or compound classes will be presented to the interested pharmaceutical industry. The SILVER consortium will be well placed to play a major role in contributing to the international effort to develop strategies to improve world health.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2010-ITN | Award Amount: 3.23M | Year: 2010

The ITN DYNAMOL will establish a powerful new approach for the preparation of nanostructures based on dynamic covalent chemistry. This approach combines the advantages of covalent synthesis (robustness of bonds) with those of non-covalent synthesis (error correction, responsiveness) without any of the disadvantages. It therefore has the potential to provide unique solutions for several important challenges in the preparation of nanostructures that still need to be addressed. The ITN unites most European leading academic experts in the area of dynamic covalent chemistry with partners from the industrial sector. Expertise of all partners encompasses the areas of supramolecular chemistry and dynamic covalent chemistry, but individual research competences are quite diverse focussing on molecularly defined nanostructures, analysis of nanostructures, and novel applications. The complementarity and diversity thus realised is crucial for successful research and training in this area. Moreover, the two full partners from the private sector, both representing small and medium-sized enterprises, and the two associated partners, one a major chemical company, will have the critical role to bridge fundamental science with application and commercialisation of the results. The objectives of the network will be achieved by recruiting 11 early stage researchers and 1 experienced researcher. A mobility program will allow the researchers to spend time in the various laboratories of the network, thus facilitating sharing of resources and expertise. Local training at the host institutions will be supplemented by a training programme containing various elements such as biannual workshops and a summer school with the participation of experts from outside the network to realise efficient exchange of information and transfer of knowledge. The ITN thus combines world-class research with a unique education to strengthen Europes prominence in the timely field of nanoscience.

Terwilliger T.C.,Los Alamos National Laboratory | Bricogne G.,Global Phasing Ltd
Acta Crystallographica Section D: Biological Crystallography | Year: 2014

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering. © 2014 International Union of Crystallography.

Wood C.S.,University of Cambridge | Ronson T.K.,University of Cambridge | Belenguer A.M.,University of Cambridge | Holstein J.J.,Global Phasing Ltd. | And 2 more authors.
Nature Chemistry | Year: 2015

Interlocked molecules possess properties and functions that depend upon their intricate connectivity. In addition to the topologically trivial rotaxanes, whose structures may be captured by a planar graph, the topologically non-trivial knots and catenanes represent some of chemistry's most challenging synthetic targets because of the three-dimensional assembly necessary for their construction. Here we report the synthesis of a cyclic [3]catenane, which consists of three mutually interpenetrating rings, via an unusual synthetic route. Five distinct building blocks self-assemble into a heteroleptic triangular framework composed of two joined Fe II 3 L 3 circular helicates. Subcomponent exchange then enables specific points in the framework to be linked together to generate the cyclic [3]catenane product. Our method represents an advance both in the intricacy of the metal-templated self-assembly procedure and in the use of selective imine exchange to generate a topologically complex product. © 2015 Macmillan Publishers Limited.

Kratzert D.,Albert Ludwigs University of Freiburg | Holstein J.J.,University of Gottingen | Holstein J.J.,Global Phasing Ltd | Krossing I.,Albert Ludwigs University of Freiburg
Journal of Applied Crystallography | Year: 2015

One of the remaining challenges in single-crystal structure refinement is the proper description of disorder in crystal structures. This paper describes a computer program that performs semi-automatic modelling of disordered moieties in SHELXL [Sheldrick (2015). Acta Cryst. C71, 3-8.]. The new program contains a database that includes molecular fragments and their corresponding stereochemical restraints, and a placement procedure to place these fragments on the desired position in the unit cell. The program is also suitable for speeding up model building of well ordered crystal structures.

Smart O.S.,Global Phasing Ltd | Womack T.O.,Global Phasing Ltd | Flensburg C.,Global Phasing Ltd | Keller P.,Global Phasing Ltd | And 4 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2012

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct target structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and - target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand. © International Union of Crystallography 2012.

Nardini M.,University of Milan | Gnesutta N.,University of Milan | Donati G.,University of Milan | Gatta R.,University of Milan | And 8 more authors.
Cell | Year: 2013

The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an α helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways. © 2013 Elsevier Inc.

Schiltz M.,Ecole Polytechnique Federale de Lausanne | Bricogne G.,Global Phasing Ltd.
Acta Crystallographica Section D: Biological Crystallography | Year: 2010

The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the sym-metry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information.

Hengrung N.,University of Oxford | El Omari K.,University of Oxford | Serna Martin I.,University of Oxford | Vreede F.T.,University of Oxford | And 9 more authors.
Nature | Year: 2015

Negative-sense RNA viruses, such as influenza, encode large, multidomain RNA-dependent RNA polymerases that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase (FluPol) is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. Replication occurs through de novo initiation and involves a complementary RNA intermediate. Currently available structures of the influenza A and B virus polymerases include promoter RNA (the 5′ and 3′ termini of viral genome segments), showing FluPol in transcription pre-initiation states. Here we report the structure of apo-FluPol from an influenza C virus, solved by X-ray crystallography to 3.9 Å, revealing a new € closed € conformation. The apo-FluPol forms a compact particle with PB1 at its centre, capped on one face by PB2 and clamped between the two globular domains of P3. Notably, this structure is radically different from those of promoter-bound FluPols. The endonuclease domain of P3 and the domains within the carboxy-terminal two-thirds of PB2 are completely rearranged. The cap-binding site is occluded by PB2, resulting in a conformation that is incompatible with transcription initiation. Thus, our structure captures FluPol in a closed, transcription pre-activation state. This reveals the conformation of newly made apo-FluPol in an infected cell, but may also apply to FluPol in the context of a non-transcribing ribonucleoprotein complex. Comparison of the apo-FluPol structure with those of promoter-bound FluPols allows us to propose a mechanism for FluPol activation. Our study demonstrates the remarkable flexibility of influenza virus RNA polymerase, and aids our understanding of the mechanisms controlling transcription and genome replication. © 2015 Macmillan Publishers Limited. All rights reserved.

Vonrhein C.,Global Phasing Ltd. | Flensburg C.,Global Phasing Ltd. | Keller P.,Global Phasing Ltd. | Sharff A.,Global Phasing Ltd. | And 4 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2011

A typical diffraction experiment will generate many images and data sets from different crystals in a very short time. This creates a challenge for the high-throughput operation of modern synchrotron beamlines as well as for the subsequent data processing. Novice users in particular may feel overwhelmed by the tables, plots and numbers that the different data-processing programs and software packages present to them. Here, some of the more common problems that a user has to deal with when processing a set of images that will finally make up a processed data set are shown, concentrating on difficulties that may often show up during the first steps along the path of turning the experiment (i.e. data collection) into a model (i.e. interpreted electron density). Difficulties such as unexpected crystal forms, issues in crystal handling and suboptimal choices of data-collection strategies can often be dealt with, or at least diagnosed, by analysing specific data characteristics during processing. In the end, one wants to distinguish problems over which one has no immediate control once the experiment is finished from problems that can be remedied a posteriori. A new software package, autoPROC, is also presented that combines third-party processing programs with new tools and an automated workflow script that is intended to provide users with both guidance and insight into the offline processing of data affected by the difficulties mentioned above, with particular emphasis on the automated treatment of multi-sweep data sets collected on multi-axis goniostats.

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