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Xu M.,University of Southern California | Beck M.,Computational and Structural Biology Unit | Alber F.,University of Southern California
Bioinformatics | Year: 2011

Motivation: Cryo electron tomography (CryoET) produces 3D density maps of biological specimen in its near native states. Applied to small cells, cryoET produces 3D snapshots of the cellular distributions of large complexes. However, retrieving this information is non-trivial due to the low resolution and low signal-to-noise ratio in tomograms. Current pattern recognition methods identify complexes by matching known structures to the cryo electron tomogram. However, so far only a small fraction of all protein complexes have been structurally resolved. It is, therefore, of great importance to develop template-free methods for the discovery of previously unknown protein complexes in cryo electron tomograms. Results: Here, we have developed an inference method for the template-free discovery of frequently occurring protein complexes in cryo electron tomograms. We provide a first proof-of-principle of the approach and assess its applicability using realistically simulated tomograms, allowing for the inclusion of noise and distortions due to missing wedge and electron optical factors. Our method is a step toward the template-free discovery of the shapes, abundance and spatial distributions of previously unknown macromolecular complexes in whole cell tomograms. © The Author(s) 2011. Published by Oxford University Press.

Lister A.L.,Northumbria University | Datta R.S.,University of California at Berkeley | Hofmann O.,Harvard University | Krause R.,Max Planck Institute for Molecular Genetics | And 3 more authors.
PLoS Computational Biology | Year: 2010

In last year's report on microblogging ISMB 2008 [1], the authors anticipated that new methods of using the Web and of reporting the conference would make live blogging even easier (http://www.bork. embl.de/∼jensen/ ismb2008/keynotes.php. html). This year, the ISMB/ECCB 2009 Web site contained all of the features of the mock-up, farmore live bloggers participated than last year, and there was increased coverage of talks and special sessions.We, in turn, look forward to the new technologies appearing on the horizon (such as Google Wave), and how both tools and bloggers will make next year's conference an even greater success. In summary, conference organizers found that microblogging added value for all conference attendees, and allowed attendees to follow the thoughts of others as well as to follow presentations that conflicted with others they wished to see. The usefulness of live blogging extends beyond the duration of the conference, remaining accessible long after the conference has closed. © 2010 Lister et al.

Asami S.,TU Munich | Asami S.,Helmholtz Center Munich | Rakwalska-Bange M.,Computational and Structural Biology Unit | Carlomagno T.,Computational and Structural Biology Unit | And 2 more authors.
Angewandte Chemie - International Edition | Year: 2013

Both protonated and deuterated samples were employed in the study of the L7Ae box C/D RNA complex by 1H-detected solid-state NMR spectroscopy. This approach yielded high-resolution spectra and was used to determine the intermolecular interface and extract structural parameters with high accuracy. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Jehle S.,Computational and Structural Biology Unit | Jehle S.,Leibniz Institute for Molecular Pharmacology | Falb M.,Computational and Structural Biology Unit | Kirkpatrick J.P.,Computational and Structural Biology Unit | And 5 more authors.
Journal of the American Chemical Society | Year: 2010

The structural investigation of large RNP complexes by X-ray crystallography can be a difficult task due to the flexibility of the RNA and of the protein-RNA interfaces, which may hinder crystallization. In these cases, NMR spectroscopy is an attractive alternative to crystallography, although the large size of typical RNP complexes may limit the applicability of solution NMR. Solid-state NMR spectroscopy, however, is not subject to any intrinsic limitations with respect to the size of the object under investigation, with restrictions imposed solely by the sensitivity of the instrumentation. In addition, it does not require large, well-ordered crystals and can therefore be applied to flexible, partially disordered complexes. Here we show for the first time that solid-state NMR spectroscopy can be used to probe intermolecular interactions at the protein-RNA interface in RNP complexes. Distances between the 15N nuclei of the protein backbone and the 31P nuclei of the RNA backbone can be measured in TEDOR experiments and used as restraints in structure calculations. The distance measurement is accurate, as proven for the test case of the L7Ae-box C/D RNA complex, for which a crystal structure is available. The results presented here reveal the as yet unexplored potential of solid-state NMR spectroscopy in the investigation of large RNP complexes. © 2010 American Chemical Society.

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