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Acta Crystallographica. Section D, Structural Biology

K K Kannan, Anders Liljas, Lars Liljas, Seved Löfgren, Michael G Rossmann, Torsten Unge
No abstract text is available yet for this article.
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Thomas L Ellinghaus, Jose H Pereira, Ryan P McAndrew, Ditte H Welner, Andy M DeGiovanni, Joel M Guenther, Huu M Tran, Taya Feldman, Blake A Simmons, Kenneth L Sale, Paul D Adams
The development of robust enzymes, in particular cellulases, is a key step in the success of biological routes to `second-generation' biofuels. The typical sources of the enzymes used to degrade biomass include mesophilic and thermophilic organisms. The endoglucanase J30 from glycoside hydrolase family 9 was originally identified through metagenomic analyses of compost-derived bacterial consortia. These studies, which were tailored to favor growth on targeted feedstocks, have already been shown to identify cellulases with considerable thermal tolerance...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Aleksandra Twarda-Clapa, Beata Labuzek, Dobroslawa Krzemien, Bogdan Musielak, Przemyslaw Grudnik, Grzegorz Dubin, Tad A Holak
Recent research has identified a potential role of the hyaluronic acid receptor stabilin-2 (Stab2) in cancer metastasis. Stab2 belongs to a group of scavenger receptors and is responsible for the clearance of more than ten ligands, including hyaluronic acid (HA). In vivo experiments on mice have shown that the absence of Stab2, or its blocking by an antibody, effectively opposes cancer metastasis, which is accompanied by an increase in the level of circulating HA. Knowledge of ligand recognition and signal transduction by Stab2 is limited and no three-dimensional structures of any protein fragments of this receptor have been solved to date...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Ian W Windsor, Ronald T Raines
Crystal structures of inactive variants of HIV-1 protease bound to peptides have revealed how the enzyme recognizes its endogenous substrates. The best of the known substrates is, however, a nonnatural substrate that was identified by directed evolution. The crystal structure of the complex between this substrate and the D25N variant of the protease is reported at a resolution of 1.1 Å. The structure has several unprecedented features, especially the formation of additional hydrogen bonds between the enzyme and the substrate...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Malwina J Radwańska, Mateusz Jaskółowski, Elena Davydova, Urszula Derewenda, Tsuyoshi Miyake, Daniel A Engel, Anthony A Kossiakoff, Zygmunt S Derewenda
The vast majority of platforms for the detection of viral or bacterial antigens rely on immunoassays, typically ELISA or sandwich ELISA, that are contingent on the availability of suitable monoclonal antibodies (mAbs). This is a major bottleneck, since the generation and production of mAbs is time-consuming and expensive. Synthetic antibody fragments (sFabs) generated by phage-display selection offer an alternative with many advantages over Fabs obtained from natural antibodies using hybridoma technology. Unlike mAbs, sFabs are generated using phage display, allowing selection for binding to specific strains or for pan-specificity, for identification of structural epitopes or unique protein conformations and even for complexes...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Steven Moussu, Sebastian Augustin, Andra Octavia Roman, Caroline Broyart, Julia Santiago
Complex cell-to-cell communication between the male pollen tube and the female reproductive organs is required for plant fertilization. A family of Catharanthus roseus receptor kinase 1-like (CrRLK1L) membrane receptors has been genetically implicated in this process. Here, crystal structures of the CrRLK1Ls ANXUR1 and ANXUR2 are reported at 1.48 and 1.1 Å resolution, respectively. The structures reveal a novel arrangement of two malectin-like domains connected by a short β-hairpin linker and stabilized by calcium ions...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Ronald E Stenkamp
Dimers of G protein-coupled receptors (GPCRs) are believed to be important for signaling with their associated G proteins. Low-resolution electron microscopy has shown rhodopsin dimers in native retinal membranes, and CXCR4 dimers have been found in several different crystal structures. Evidence for dimers of other GPCRs is more indirect. An alternative to computational modeling studies is to search for parallel dimers in the packing environments of the reported crystal structures of GPCRs. Two major structural types of GPCR dimers exist (as predicted by others), but there is considerable structural variation within each cluster...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Andreas Schmitt, Florian Hamann, Piotr Neumann, Ralf Ficner
The DEAH-box ATPase Prp2 plays a key role in the activation of the spliceosome as it promotes the transition from the Bact to the catalytically active B* spliceosome. Here, four crystal structures of Prp2 are reported: one of the nucleotide-free state and three different structures of the ADP-bound state. The overall conformation of the helicase core, formed by two RecA-like domains, does not differ significantly between the ADP-bound and the nucleotide-free states. However, intrinsic flexibility of Prp2 is observed, varying the position of the C-terminal domains with respect to the RecA domains...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Eugeny M Osipov, Anastasia V Lilina, Stanislav I Tsallagov, Tatyana N Safonova, Dimitry Y Sorokin, Tamara V Tikhonova, Vladimir O Popov
Flavocytochrome c sulfide dehydrogenase from Thioalkalivibrio paradoxus (TpFCC) is a heterodimeric protein consisting of flavin- and monohaem c-binding subunits. TpFCC was co-purified and co-crystallized with the dimeric copper-binding protein TpCopC. The structure of the TpFCC-(TpCopC)2 complex was determined by X-ray diffraction at 2.6 Å resolution. The flavin-binding subunit of TpFCC is structurally similar to those determined previously, and the structure of the haem-binding subunit is similar to that of the N-terminal domain of dihaem FCCs...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Pavel V Afonine, Paul D Adams, Alexandre Urzhumtsev
TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63-76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Jouko J Virtanen, Yang Zhang
Molecular replacement (MR) has commonly been employed to derive the phase information in protein crystal X-ray diffraction, but its success rate decreases rapidly when the search model is dissimilar to the target. MR-REX has been developed to perform an MR search by replica-exchange Monte Carlo simulations, which enables cooperative rotation and translation searches and simultaneous clash and occupancy optimization. MR-REX was tested on a set of 1303 protein structures of different accuracies and successfully placed 699 structures at positions that have an r...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Adam J Simpkin, Felix Simkovic, Jens M H Thomas, Martin Savko, Andrey Lebedev, Ville Uski, Charles Ballard, Marcin Wojdyr, Rui Wu, Ruslan Sanishvili, Yibin Xu, María Natalia Lisa, Alejandro Buschiazzo, William Shepard, Daniel J Rigden, Ronan M Keegan
The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures...
July 1, 2018: Acta Crystallographica. Section D, Structural Biology
Florian M Rossmann, Morgan Beeby
In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high-throughput, medium-resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Joseph Atherton, Melissa Stouffer, Fiona Francis, Carolyn A Moores
The microtubule cytoskeleton is involved in many vital cellular processes. Microtubules act as tracks for molecular motors, and their polymerization and depolymerization can be harnessed to generate force. The structures of microtubules provide key information about the mechanisms by which their cellular roles are accomplished and the physiological context in which these roles are performed. Cryo-electron microscopy allows the visualization of in vitro-polymerized microtubules and has provided important insights into their overall morphology and the influence of a range of factors on their structure and dynamics...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Ieva Drulyte, Rachel M Johnson, Emma L Hesketh, Daniel L Hurdiss, Charlotte A Scarff, Sebastian A Porav, Neil A Ranson, Stephen P Muench, Rebecca F Thompson
Cryo-electron microscopy (cryo-EM) can now be used to determine high-resolution structural information on a diverse range of biological specimens. Recent advances have been driven primarily by developments in microscopes and detectors, and through advances in image-processing software. However, for many single-particle cryo-EM projects, major bottlenecks currently remain at the sample-preparation stage; obtaining cryo-EM grids of sufficient quality for high-resolution single-particle analysis can require the careful optimization of many variables...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Thomas C Terwilliger, Oleg V Sobolev, Pavel V Afonine, Paul D Adams
An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams
This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Tristan Ian Croll
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Max T B Clabbers, Tim Gruene, James M Parkhurst, Jan Pieter Abrahams, David G Waterman
Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
Robert A Nicholls, Michal Tykac, Oleg Kovalevskiy, Garib N Murshudov
Recent advances in instrumentation and software have resulted in cryo-EM rapidly becoming the method of choice for structural biologists, especially for those studying the three-dimensional structures of very large macromolecular complexes. In this contribution, the tools available for macromolecular structure refinement into cryo-EM reconstructions that are available via CCP-EM are reviewed, specifically focusing on REFMAC5 and related tools. Whilst originally designed with a view to refinement against X-ray diffraction data, some of these tools have been able to be repurposed for cryo-EM owing to the same principles being applicable to refinement against cryo-EM maps...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
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