nils-herrmann/clean_scirepeval huggingface dataset:
Quantitative morphological analysis of arrestin2 clustering upon G protein-coupled receptor stimulation by super-resolution microscopy.
Venue: Journal of structural biology

Clustering of arrestins upon G protein-coupled receptor stimulation is a phenomenon that is well-known but difficult to describe quantitatively due to the size of the clusters close to the diffraction limit of visible light. We introduce a general method to quantitatively investigate the clustering of arrestin following stimulation of the C-C chemokine receptor 5 (CCR5) using single-molecule super-resolution imaging and coordinate and image-based cluster analysis. We investigated the effect of potent anti-HIV ligands of CCR5 with different pharmacological profiles on arrestin2 cluster formation and found that only the ligands capable of inducing CCR5 internalization induced arrestin2 recruitment and clustering. We further demonstrate that the fraction of arrestin2 molecules found in clusters larger than 100nm correlates with the magnitude of ligand-induced CCR5 internalization, but not with G protein activation, indicating that recruitment of arrestin2 to CCR5 is independent of G protein activation. Pre-treatment of the cells with the drug cytochalasin D, which blocks actin polymerization, led to the formation of larger clusters, whereas the inhibitor of microtubule polymerization nocodazole had little effect on arrestin2 recruitment, suggesting an active role of actin in the organization and dynamics of these aggregates.
Bone quality around bioactive silica-based coated stainless steel implants: analysis by micro-Raman, XRF and XAS techniques.
Venue: Journal of structural biology

Surface modification of surgical stainless steel implants by sol gel coatings has been proposed as a tool to generate a surface that besides being protective could also create a "bioactive" interface to generate a natural bonding between the metal surface and the existing bone. The aim of this work is to analyze the quality and bone formation around hybrid bioactive coatings containing glass-ceramic particles, made by sol-gel process on 316L stainless steel used as permanent implant in terms of mineralization, calcium content and bone maturity with micro Raman, X-ray microfluorescence and X-ray absorption techniques. Uncoated implants seem to generate a thin bone layer at the beginning of osseointegration process and then this layer being separated from the surface with time. The hybrid coatings without glass-ceramic particles generate new bone around implants, with high concentration of Ca and P at the implant/tissue interface. This fact seems to be related with the presence of silica nanoparticles in the layer. The addition of bioactive particles promotes and enhances the bone quality with a homogeneous Ca and P content and a low rate of beta carbonate substitution and crystallinity, similar to young and mechanical resistant bone.
Crystal structure of rat intestinal alkaline phosphatase--role of crown domain in mammalian alkaline phosphatases.
Venue: Journal of structural biology

Intestinal alkaline phosphatases (IAPs) are involved in the cleavage of phosphate prodrugs to liberate the drug for absorption in the intestine. To facilitate in vitro characterization of phosphate prodrugs, we have cloned, expressed, purified and characterized IAPs from rat and cynomolgus monkey (rIAP and cIAP respectively) which are important pre-clinical species for drug metabolism studies. The recombinant rat and monkey enzymes expressed in Sf9 insect cells (IAP-Ic) were found to be glycosylated and active. Expression of rat IAP in Escherichia coli (rIAP-Ec) led to ~200-fold loss of activity that was partially recovered by the addition of external Zn(2+) and Mg(2+) ions. Crystal structures of rIAP-Ec and rIAP-Ic were determined and they provide rationale for the discrepancy in enzyme activities. Rat IAP-Ic retains its activity in presence of both Zn(2+) and Mg(2+) whereas activity of most other alkaline phosphatases (APs) including the cIAP was strongly inhibited by excess Zn(2+). Based on our crystal structure, we hypothesized the residue Q317 in rIAP, present within 7 Å of the Mg(2+) at M3, to be important for this difference in activity. The Q317H rIAP and H317Q cIAP mutants showed reversal in effect of Zn(2+), corroborating the hypothesis. Further analysis of the two structures indicated a close linkage between glycosylation and crown domain stability. A triple mutant of rIAP, where all the three putative N-linked glycosylation sites were mutated showed thermal instability and reduced activity.
Xmipp 3.0: an improved software suite for image processing in electron microscopy.
Venue: Journal of structural biology

Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter "wizards" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es.
Zernike phase contrast cryo-electron tomography of whole bacterial cells.
Venue: Journal of structural biology

Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution.
Tissue specific specialization of the nanoscale architecture of Arabidopsis.
Venue: Journal of structural biology

The Arabidopsis stem is composed of five tissues - the pith, xylem, phloem, cortex and epidermis - each of which fulfills specific roles in support of the growth and survival of the organism. The lignocellulosic scaffolding of cell walls is specialized to provide optimal support for the diverse functional roles of these layers, but little is known about this specialization. X-ray scattering can be used to study this tissue-specific diversity because the cellulosic components of the cell walls give rise to recognizable scattering features interpretable in terms of the underlying molecular architecture and distinct from the largely unoriented scatter from other constituents. Here we use scanning X-ray microdiffraction from thin sections to characterize the diversity of molecular architecture in the Arabidopsis stem and correlate that diversity to the functional roles the distinct tissues of the stem play in the growth and survival of the organism.
gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.
Venue: Journal of structural biology

Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) to accelerate both the translational and rotational parts of the correlation search. In particular, by using the GPU's special texture memory hardware to rotate 3D voxel grids, the cost of rotating large 3D density maps is almost completely eliminated. Compared to performing 3D correlations on one core of a contemporary central processor unit (CPU), running gEMfitter on a modern GPU gives up to 26-fold speed-up. Furthermore, using our parallel processing framework, this speed-up increases linearly with the number of CPUs or GPUs used. Thus, it is now possible to use routinely more robust but more expensive 3D correlation techniques. When tested on low resolution experimental cryo-EM data for the GroEL-GroES complex, we demonstrate the satisfactory fitting results that may be achieved by using a locally normalised cross-correlation with a Laplacian pre-filter, while still being up to three orders of magnitude faster than the well-known COLORES program.
Metal-mediated crystallization of the xylose transporter XylE from Escherichia coli in three different crystal forms.
Venue: Journal of structural biology

XylE is a major facilitator (MFS) xylose transporter, which is homologous to the mammalian glucose transporters (GLUT family). We have previously reported the structure of XylE in fully inward open and partially occluded inward open conformations in space groups P61 and C2, respectively. Here we present the crystallization of a third crystal form, P212121 (~4 Å resolution), also representing an inward facing conformation, and analyze all three forms in terms of crystallization conditions and packing. The crystallization conditions were generally very similar with only slight changes needed to favor one form over another, e.g. the presence of lanthanide ions greatly favors C2 over P212121 under otherwise identical conditions. Cadmium was essential for crystallization of all three forms, which indeed all contain a Cd(2+) ion in a crystal packing interface, though surprisingly in different positions. Cadmium was also found to bind to XylE in solution. The diffraction data were highly anisotropic for all forms, reflecting a lack of ordered crystal contacts along one or two of the cell axes. The best diffracting directions thus consistently correlate with the presence of ordered contacts, most of which are metal-mediated. The data presented here highlight the utility of metal ions in membrane protein crystallization and suggest that metal site engineering may be a productive path towards obtaining additional crystal forms of XylE and other membrane proteins.
Family of phenylacetyl-CoA monooxygenases differs in subunit organization from other monooxygenases.
Venue: Journal of structural biology

The phenylacetate degradation pathway is present in a wide range of microbes. A key component of this pathway is the four-subunit phenylacetyl-coenzyme A monooxygenase complex (PA-CoA MO, PaaACBE) that catalyzes the insertion of an oxygen in the aromatic ring of PA. This multicomponent enzyme represents a new family of monooxygenases. We have previously determined the structure of the PaaAC subcomplex of catalytic (A) and structural (C) subunits and shown that PaaACB form a stable complex. The PaaB subunit is unrelated to the small subunits of homologous monooxygenases and its role and organization of the PaaACB complex is unknown. From low-resolution crystal structure, electron microscopy and small angle X-ray scattering we show that the PaaACB complex forms heterohexamers, with a homodimer of PaaB bridging two PaaAC heterodimers. Modeling the interactions of reductase subunit PaaE with PaaACB suggested that a unique and conserved 'lysine bridge' constellation near the Fe-binding site in the PaaA subunit (Lys68, Glu49, Glu72 and Asp126) may form part of the electron transfer path from PaaE to the iron center. The crystal structure of the PaaA(K68Q/E49Q)-PaaC is very similar to the wild-type enzyme structure, but when combined with the PaaE subunit the mutant showed 20-50 times reduced activity, supporting the functional importance of the 'lysine bridge'.
Atomic force microscopy studies of APOBEC3G oligomerization and dynamics.
Venue: Journal of structural biology

The DNA cytosine deaminase APOBEC3G (A3G) is a two-domain protein that binds single-stranded DNA (ssDNA) largely through its N-terminal domain and catalyzes deamination using its C-terminal domain. A3G is considered an innate immune effector protein, with a natural capacity to block the replication of retroviruses such as HIV and retrotransposons. However, knowledge about its biophysical properties and mechanism of interaction with DNA are still limited. Oligomerization is one of these unclear issues. What is the stoichiometry of the free protein? What are the factors defining the oligomeric state of the protein? How does the protein oligomerization change upon DNA binding? How stable are protein oligomers? We address these questions here using atomic force microscopy (AFM) to directly image A3G protein in a free-state and in complexes with DNA, and using time-lapse AFM imaging to characterize the dynamics of A3G oligomers. We found that the formation of oligomers is an inherent property of A3G and that the yield of oligomers depends on the protein concentration. Oligomerization of A3G in complexes with ssDNA follows a similar pattern: the higher the protein concentrations the larger oligomers sizes. The specificity of A3G binding to ssDNA does not depend on stoichiometry. The binding of large A3G oligomers requires a longer ssDNA substrate; therefore, much smaller oligomers form complexes with short ssDNA. A3G oligomers dissociate spontaneously into monomers and this process primarily occurs through a monomer dissociation pathway.
Assembly of the Leishmania amazonensis flagellum during cell differentiation.
Venue: Journal of structural biology

The flagellar cytoskeleton of Leishmania promastigotes contains the canonical 9+2 microtubular axoneme and a filamentous structure, the paraflagellar rod (PFR), which is present alongside the axoneme. In contrast to promastigotes, which contain a long and motile flagellum, the amastigote form of Leishmania displays a short flagellum without a PFR that is limited to the flagellar pocket domain. Here, we investigated the biogenesis of the Leishmania flagellum at 0, 4, 6 and 24h of differentiation. Light and electron microscopy observations of the early stages of L. amazonensis differentiation showed that the intermediate forms presented a short and wider flagellum that did not contain a PFR and presented reduced motion. 3D-reconstruction analysis of electron tomograms revealed the presence of vesicles and electron-dense aggregates at the tip of the short flagellum. In the course of differentiation, cells were able to adhere and proliferate with a doubling time of about 6h. The new flagellum emerged from the flagellar pocket around 4h after initiation of cell cycle. Close contact between the flagellar membrane and the flagellar pocket membrane was evident in the intermediate forms. At a later stage of differentiation, intermediate cells exhibited a longer flagellum (shorter than in promastigotes) that contained a PFR and electron dense aggregates in the flagellar matrix. In some cells, PFR profiles were observed inside the flagellar pocket. Taken together, these data contribute to the understanding of flagellum biogenesis and organisation during L. amazonensis differentiation.
Electron microscopy analysis of a disaccharide analog complex reveals receptor interactions of adeno-associated virus.
Venue: Journal of structural biology

Mechanistic studies of macromolecular complexes often feature X-ray structures of complexes with bound ligands. The attachment of adeno-associated virus (AAV) to cell surface glycosaminoglycans (GAGs) is an example that has not proven amenable to crystallography, because the binding of GAG analogs disrupts lattice contacts. The interactions of AAV with GAGs are of interest in mediating the cell specificity of AAV-based gene therapy vectors. Previous electron microscopy led to differing conclusions on the exact binding site and the existence of large ligand-induced conformational changes in the virus. Conformational changes are expected during cell entry, but it has remained unclear whether the electron microscopy provided evidence of their induction by GAG-binding. Taking advantage of automated data collection, careful processing and new methods of structure refinement, the structure of AAV-DJ complexed with sucrose octasulfate is determined by electron microscopy difference map analysis to 4.8Å resolution. At this higher resolution, individual sulfate groups are discernible, providing a stereochemical validation of map interpretation, and highlighting interactions with two surface arginines that have been implicated in genetic studies. Conformational changes induced by the SOS are modest and limited to the loop most directly interacting with the ligand. While the resolution attainable will depend on sample order and other factors, there are an increasing number of macromolecular complexes that can be studied by cryo-electron microscopy at resolutions beyond 5Å, for which the approaches used here could be used to characterize the binding of inhibitors and other small molecule effectors when crystallography is not tractable.
Binding sites and hydrophobic pockets in Human Thioredoxin 1 determined by normal mode analysis.
Venue: Journal of structural biology

The Thioredoxin (Trx) system plays important roles in several diseases (e.g. cancer, viral infections, cardiovascular and neurodegenerative diseases). Therefore, there is a therapeutic interest in the design of modulators of this system. In this work, we used normal mode analysis to identify putative binding site regions for Human Trx1 that arise from global motions. We identified three possible inhibitor's binding regions that corroborate previous experimental findings. We show that intrinsic motions of the protein are related to the exposure of hydrophobic regions and non-active site cysteines that could constitute new binding sites for inhibitors.
Maximizing the potential of electron cryomicroscopy data collected using direct detectors.
Venue: Journal of structural biology

Single-particle electron cryomicroscopy is undergoing a technical revolution due to the recent developments of direct detectors. These new recording devices detect electrons directly (i.e. without conversion into light) and feature significantly improved detective quantum efficiencies and readout rates as compared to photographic films or CCDs. We evaluated here the potential of one such detector (Gatan K2 Summit) to enable the achievement of near-atomic resolution reconstructions of biological specimens when coupled to a widely used, mid-range transmission electron microscope (FEI TF20 Twin). Compensating for beam-induced motion and stage drift provided a 4.4Å resolution map of Sulfolobus turreted icosahedral virus (STIV), which we used as a test particle in this study. Several motion correction and dose fractionation procedures were explored and we describe their influence on the resolution of the final reconstruction. We also compared the quality of this data to that collected with a FEI Titan Krios microscope equipped with a Falcon I direct detector, which provides a benchmark for data collected using a high-end electron microscope.
Chaplins of Streptomyces coelicolor self-assemble into two distinct functional amyloids.
Venue: Journal of structural biology

Chaplins are small, secreted proteins of streptomycetes that play instrumental roles in the formation of aerial hyphae and attachment of hyphae to surfaces. Here we show that the purified proteins self-assemble at a water/air interface into an asymmetric and amphipathic protein membrane that has an amyloid nature. Cryo-tomography reveals that the hydrophilic surface is relatively smooth, while the hydrophobic side is highly structured and characterized by the presence of small fibrils, which are similar to those observed on the surfaces of aerial hyphae. Interestingly, our work also provides evidence that chaplins in solution assemble into amyloid fibrils with a distinct morphology. These hydrophilic fibrils strongly resemble the structures known to be involved in attachment of Streptomyces hyphae to surfaces. These data for the first time show the assembly of bacterial proteins into two distinct amyloid structures that have different and relevant functions in vivo.
Three-dimensional network of Drosophila brain hemisphere.
Venue: Journal of structural biology

The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built by tracing the three-dimensional distribution of X-ray absorption coefficients. The obtained models of neuronal processes were classified into groups on the basis of their three-dimensional structures. These classified groups correspond to neuronal tracts that send long-range projections or repeated structures of the optic lobe. The skeletonized model is also composed of neuronal processes that could not be classified into the groups. The distribution of these unclassified structures correlates with the distribution of contacts between neuronal processes. This suggests that neurons that cannot be classified into typical structures should play important roles in brain functions. The quantitative description of the brain network provides a basis for structural and statistical analyses of the Drosophila brain. The challenge is to establish a methodology for reconstructing the brain network in a higher-resolution image, leading to a comprehensive understanding of the brain structure.
Crystal structure of the effector protein XOO4466 from Xanthomonas oryzae.
Venue: Journal of structural biology

Many Gram-negative bacteria deliver their virulence factors into host cells through a secretion system. Those factors, called effector proteins, are involved in the pathogenicity in host cells by interfering with various cellular events. The phytopathogen Xanthomonas oryzae pv. oryzae uses a type III secretion system to inject its effectors, but the functional roles of these proteins remain largely uncharacterized. Here, we determined a crystal structure of XOO4466, an effector from X. oryzae pv. oryzae, and performed a functional analysis. We determined that XOO4466 is similar in sequence to Xanthomonas outer protein Q, a putative nucleoside hydrolase (NH). The overall structure of XOO4466 is homologous to that of NHs, including a metal-binding site, but differs in its oligomeric state and active site topology. Further analysis indicated that antiparallel β-strands commonly found in NHs adjacent to the active site loop are replaced in XOO4466 with a short loop, causing the active site loop to adopt a conformation distinct from that of NHs. Thus, the catalytic residues emanating from the respective active site loop of NHs are absent in the putative active site of XOO4466. Consistent with these structural features, a functional assay indicated that XOO4466 does not exhibit NH activity and possibly catalyzes yet unknown reactions.