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Trempe J.-F.,McGill University | Brown N.R.,Laboratory of Molecular Biophysics | Noble M.E.M.,Laboratory of Molecular Biophysics | Endicott J.A.,Laboratory of Molecular Biophysics
Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6 Å resolution. The structure reveals an ordered isopeptide bond in a trans configuration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2 is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage. © 2010 International Union of Crystallography All rights reserved. Source

Liang M.,SLAC | Williams G.J.,SLAC | Williams G.J.,Brookhaven National Laboratory | Messerschmidt M.,SLAC | And 19 more authors.
Journal of Synchrotron Radiation

The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100nm focus and one a 1μm focus, are available, each with multiple diagnostics, sample injection, pump-probe and detector capabilities. The flexibility of CXI has enabled it to host a diverse range of experiments, from biological to extreme matter. Source

Sinclair J.C.,Laboratory of Molecular Biophysics | Davies K.M.,Laboratory of Molecular Biophysics | Venien-Bryan C.,Laboratory of Molecular Biophysics | Venien-Bryan C.,University Pierre and Marie Curie | Noble M.E.M.,Laboratory of Molecular Biophysics
Nature Nanotechnology

The self-assembly of supramolecular structures that are ordered on the nanometre scale is a key objective in nanotechnology. DNA 1-4 and peptide 5-7 nanotechnologies have produced various two- and three-dimensional structures, but protein molecules have been underexploited in this area of research. Here we show that the genetic fusion of subunits from protein assemblies that have matching rotational symmetry generates species that can self-assemble into well-ordered, pre-determined one- and two-dimensional arrays that are stabilized by extensive intermolecular interactions. This new class of supramolecular structure provides a way to manufacture biomaterials with diverse structural and functional properties. © 2011 Macmillan Publishers Limited. All rights reserved. Source

Chaikuad A.,Research Campus Building | Pilka E.S.,Research Campus Building | De Riso A.,Laboratory of Molecular Biophysics | Von Delft F.,Research Campus Building | And 5 more authors.
BMC Structural Biology

Backround: Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated. Results: The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β- hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids. Conclusions: The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference. Together, the structural knowledge will aid in the development of enzyme- /family-specific aminopeptidase inhibitors. © 2012 Chaikuad et al.; licensee BioMed Central Ltd. Source

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