nils-herrmann/clean_scirepeval huggingface dataset:
Mineralization and collagen orientation throughout aging at the vertebral endplate in the human lumbar spine.
Venue: Journal of structural biology

The human vertebral body and intervertebral disc interface forms the region where the cartilaginous endplate, annulus fibrosis and bone of the vertebral body are connected through an intermediate calcified cartilage layer. While properties of both the vertebral body and components of the disc have been extensively studied, limited quantitative data exists describing the microstructure of the vertebral body-intervertebral disc interface in the spine throughout development and degeneration. Quantitative backscattered scanning electron and second harmonic generation confocal imaging were used to collect quantitative data describing the mineral content and collagen fiber orientation across the interface, respectively. Specimens spanned ages 56 days to 84 years and measurements were taken across the vertebral endplate at the outer annulus, inner annulus and nucleus pulposis. In mature and healthy endplates, collagen fibers span the calcified cartilage layer in all regions, including the endplate adjacent to the central nucleus pulposis. We also observed an abrupt transition from high mineral volume fractions (35-50%) to 0% over short distances measuring 3-15 microns in width across the transition from calcified cartilage to unmineralized cartilage. The alignment of collagen fibers at the outer annulus and thickness of the CC layer indicated that collagen fiber mineralization adjacent to the bone may serve to anchor the soft tissue without a gradual change in material properties. Combining backscattered scanning electron microscopy and second harmonic generation imaging on the same sections thus enable a novel assessment of morphology and properties in both mineralized and soft tissues at the vertebral body-intervertebral disc throughout development and aging.
iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.
Venue: Journal of structural biology

Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures into electron microscopy (EM) density maps. The proposed methodology was validated using a benchmark of simulated cases, highlighting its robustness over the full range of EM resolutions and even over coarse-grained representations. A systematic comparison with other methods further showcased the advantages of this proposed methodology, especially at medium to lower resolutions. Using this method, computational costs and potential overfitting problems are naturally reduced by constraining the search in low-frequency NMA space, where covalent geometry is implicitly maintained. This method also effectively captures the macromolecular changes of a representative set of experimental test cases. We believe that this novel approach will extend the currently available EM hybrid methods to the atomic-level interpretation of large conformational changes and their functional implications.
Methods for testing Zernike phase plates and a report on silicon-based phase plates with reduced charging and improved ageing characteristics.
Venue: Journal of structural biology

Imaging with Zernike phase plates is increasingly being used in cryo-TEM tomography and cryo-EM single-particle applications. However, rapid ageing of the phase plates, together with the cost and effort in producing them, present serious obstacles to widespread adoption. We are experimenting with phase plates based on silicon chips that have thin windows; such phase plates could be mass-produced and made available at moderate cost. The windows are coated with conductive layers to reduce charging, and this considerably extends the useful life of the phase plates compared to traditional pure-carbon phase plates. However, a compromise must be reached between robustness and transmission through the phase-plate film. Details are given on testing phase-plate performance by means of imaging an amorphous thin film and evaluating the power spectra of the images.
Influence of canonical structure determining residues on antibody affinity and stability.
Venue: Journal of structural biology

A number of light and heavy chain canonical residue core redesigns were made in a therapeutic antibody (AQC2, anti-VLA1) Fab to explore the consequences to binding affinity and stability. These positions are all loop supporting, primarily CDR1 residues which do not directly contact the antigen. Structure based methods were used with and without consensus sequence information. 30 constructs were made, 24 expressed, and 70% of the designs using consensus sequence information retained binding affinity. Some success maintaining stability with more extreme redesigns suggests a surprising tolerance to mutation, though it often comes at the cost of loss of binding affinity and presumed loop conformation changes. In concordance with the expected need to present an ordered surface for binding, a relationship between decreased affinity and decreased stability was observed. Overpacking the core tends to destabilize the molecule and should be avoided.
Optimal and fast rotational alignment of volumes with missing data in Fourier space.
Venue: Journal of structural biology

Electron tomography of intact cells has the potential to reveal the entire cellular content at a resolution corresponding to individual macromolecular complexes. Characterization of macromolecular complexes in tomograms is nevertheless an extremely challenging task due to the high level of noise, and due to the limited tilt angle that results in missing data in Fourier space. By identifying particles of the same type and averaging their 3D volumes, it is possible to obtain a structure at a more useful resolution for biological interpretation. Currently, classification and averaging of sub-tomograms is limited by the speed of computational methods that optimize alignment between two sub-tomographic volumes. The alignment optimization is hampered by the fact that the missing data in Fourier space has to be taken into account during the rotational search. A similar problem appears in single particle electron microscopy where the random conical tilt procedure may require averaging of volumes with a missing cone in Fourier space. We present a fast implementation of a method guaranteed to find an optimal rotational alignment that maximizes the constrained cross-correlation function (cCCF) computed over the actual overlap of data in Fourier space.
Influence of electron dose rate on electron counting images recorded with the K2 camera.
Venue: Journal of structural biology

A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.
Computational design of protein-small molecule interfaces.
Venue: Journal of structural biology

The computational design of proteins that bind small molecule ligands is one of the unsolved challenges in protein engineering. It is complicated by the relatively small size of the ligand which limits the number of intermolecular interactions. Furthermore, near-perfect geometries between interacting partners are required to achieve high binding affinities. For apolar, rigid small molecules the interactions are dominated by short-range van der Waals forces. As the number of polar groups in the ligand increases, hydrogen bonds, salt bridges, cation-π, and π-π interactions gain importance. These partial covalent interactions are longer ranged, and additionally, their strength depends on the environment (e.g. solvent exposure). To assess the current state of protein-small molecule interface design, we benchmark the popular computer algorithm Rosetta on a diverse set of 43 protein-ligand complexes. On average, we achieve sequence recoveries in the binding site of 59% when the ligand is allowed limited reorientation, and 48% when the ligand is allowed full reorientation. When simulating the redesign of a protein binding site, sequence recovery among residues that contribute most to binding was 52% when slight ligand reorientation was allowed, and 27% when full ligand reorientation was allowed. As expected, sequence recovery correlates with ligand displacement.
Plasmid- and chromosomal genes-encoded two separate O-polysaccharide chains of Salmonella Uccle (O:3,54)--structural elucidation.
Venue: Journal of structural biology

The bacterium Salmonella Uccle belongs to serotype O:54 in the Kauffmann'a-White scheme. Group O:54 is unique among the serogroups belonging to the genus Salmonella. Normally, the enzymes involved in the biosynthesis of the repeating units of somatic antigen are encoded by a set of genes, located in the region of the bacterial chromosome. Expression of O54 factor is associated with the presence of the plasmid. Factor O54 can be lost spontaneously in the subcultures of some serotypes. In these cases, the O54 negative variants become indistinguishable from the serotypes classified in other groups. We noticed lower activity of LPS-u O:3,54 with rabbit sera against antigens O:3, when compared with the activity of sera anti-A:54, which may indicate a partial inhibition of the expression of factor O:3 on the surface of the bacterial cell. The main aim of our study was to answer the question whether the products of different biosynthetic pathways combine on the outer side of the cytoplasmic membrane, thus forming a single chain or separate chains. Therefore, the O-polysaccharides (O-antigen) of Salmonella Uccle O:3,54 were isolated by mild acid degradation of both obtained LPSs and their structure was established using sugar and methylation analysis and NMR spectroscopy. The primary structure of two separate O-polysaccharide chains isolated from Salmonella Uccle were established.
One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions.
Venue: Journal of structural biology

The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.
Preface for the special issue celebrating Stephen Weiner's 65th birthday.
Venue: Journal of structural biology

The products of biomineralization have attracted the attention and the curiosity of scientists for many years. The origin of biomineralization as a scientific discipline may be tracked to the 19th century, with early work on bone and on sponge spicules and the recognition that organic molecules may influence the growth of inorganic crystals. But the blooming of general interest in biomineralization really started in the second half of the 20th century. Steve Weiner first heard about biomineralization in the early seventies from a lecture of Heinz Lowenstam in Jerusalem, and decided to join Heinz in Caltech for his PhD: since then, Steve never ceased to be fascinated by biomineralization and to work in this field, and with good reason. Having worked with Steve for many years, in the field and in the lab, we know and share his passion and excitement. Heinz said in an interview with Heidi Aspaturian in 1989: ‘‘I am pleased with one thing: that I myself, with the help of my former students, Steve in particular, have gotten people who work on. . . bone and teeth to look at their work in the broader context of biomineralization. I have tried to show them that their work is only a small part of the whole biomineralization process, and that if one looks at the broader picture and gets information on how these processes work, one might get feedback in terms of better understanding what is going on...’’. Biomineralization is the science of how inorganic and also organic substances are deposited and controlled by living systems and is, thus, inherently multidisciplinary. In 1989, Steve and Heinz listed in the introduction of their book ‘‘On biomineralization’’ the scientific disciplines that are touched by biomineralization: evolution, paleontology, oceanography, sedimentology, materials, dentistry, orthopedics and archeology. Today we should at least add to that list biomimetics, mechanics and of course structural biology. Starting from the 1970s and to this day, the developments in molecular biology provided an increasing amount of knowledge on the macromolecules involved in the interactions with, and the control of, the mineral phases. The advances in this area were predictably much slower than in other areas of biology, because of the multitude and the complexity of the macromolecules involved, and because of the difficulties emanating from their association with mineral: there is still much to do. The development of new characterization tools and groundbreaking advances in electron microscopy provide us today with insights into what occurs in mineralizing tissues at the supra-molecular level under close to physiological conditions. New sophisticated spectroscopic techniques provide us with the possibility to obtain fingerprints of minerals and of their development, of organic matrix profiles, of the interfaces and interphases between them at nanometer resolu-
A microstructural study of individual nacre tablet of Pinctada maxima.
Venue: Journal of structural biology

Nacre tablets from the shell of Pinctada maxima were studied with SEM, TEM and STEM. The systematic nanolath morphology on the (001) surface of nacre tablets was observed after acidic etching and mechanical polishing. The nanolaths were along the [100] crystallographic orientation of aragonite crystal. The (010) and (100) cross section surfaces of the nacre tablets showed nanolath and nanograin morphologies, respectively, which was consistent with [100] crystallographic orientation of nanolath on the (001) surface. Sheet-like defects with low mass density were observed on the (001) plane inside nacre tablets and were considered to be the cause of nanolath morphology revealed on the surfaces by acidic etching and mechanical polishing. On the other hand, large block [110] twins that divide the nacre tablets into two sectors were identified. The implication of these twins on the understanding to the crystallization mechanism of nacre tablets was discussed.
Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.
Venue: Journal of structural biology

Three-dimensional reconstruction of biological specimens using electron microscopy by single particle methodologies requires the identification and extraction of the imaged particles from the acquired micrographs. Automatic and semiautomatic particle selection approaches can localize these particles, minimizing the user interaction, but at the cost of selecting a non-negligible number of incorrect particles, which can corrupt the final three-dimensional reconstruction. In this work, we present a novel particle quality assessment and sorting method that can separate most erroneously picked particles from correct ones. The proposed method is based on multivariate statistical analysis of a particle set that has been picked previously using any automatic or manual approach. The new method uses different sets of particle descriptors, which are morphology-based, histogram-based and signal to noise analysis based. We have tested our proposed algorithm with experimental data obtaining very satisfactory results. The algorithm is freely available as a part of the Xmipp 3.0 package [http://xmipp.cnb.csic.es].
Crystallographic control on the substructure of nacre tablets.
Venue: Journal of structural biology

Nacre tablets of mollusks develop two kinds of features when either the calcium carbonate or the organic portions are removed: (1) parallel lineations (vermiculations) formed by elongated carbonate rods, and (2) hourglass patterns, which appear in high relief when etched or in low relief if bleached. In untreated tablets, SEM and AFM data show that vermiculations correspond to aligned and fused aragonite nanogloblules, which are partly surrounded by thin organic pellicles. EBSD mapping of the surfaces of tablets indicates that the vermiculations are invariably parallel to the crystallographic a-axis of aragonite and that the triangles are aligned with the b-axis and correspond to the advance of the {010} faces during the growth of the tablet. According to our interpretation, the vermiculations appear because organic molecules during growth are expelled from the a-axis, where the Ca-CO3 bonds are the shortest. In this way, the subunits forming nacre merge uninterruptedly, forming chains parallel to the a-axis, whereas the organic molecules are expelled to the sides of these chains. Hourglass patterns would be produced by preferential adsorption of organic molecules along the {010}, as compared to the {100} faces. A model is presented for the nanostructure of nacre tablets. SEM and EBSD data also show the existence within the tablets of nanocrystalline units, which are twinned on {110} with the rest of the tablet. Our study shows that the growth dynamics of nacre tablets (and bioaragonite in general) results from the interaction at two different and mutually related levels: tablets and nanogranules.
Detection of soluble co-factor dependent protein expression in vivo: application to the 4'-phosphopantetheinyl transferase PptT from Mycobacterium tuberculosis.
Venue: Journal of structural biology

The need for early-on diagnostic tools to assess the folding and solubility of expressed protein constructs in vivo is of great interest when dealing with recalcitrant proteins. In this paper, we took advantage of the picomolar sensitivity of the bipartite GFP1-10/GFP11 system to investigate the solubility of the Mycobacterium tuberculosis 4'-phosphopantetheinyl transferase PptT, an enzyme essential for the viability of the tubercle bacillus. In vivo and in vitro complementation assays clearly showed the improved solubility of the full-length PptT compared to its N- and C-terminally truncated counterparts. However, initial attempts to purify the full-length enzyme overexpressed in Escherichia coli cells were hampered by aggregation issues overtime that caused the protein to precipitate within hours. The fact that the naturally occurring Coenzyme A and Mg(2+), essentials for PptT to carry out its function, could play a role in stabilizing the enzyme was confirmed using DSF experiments. In vitro activity assays were performed using the ACP substrate from the type I polyketide synthase PpsC from M. tuberculosis, a 2188 amino-acid enzyme that plays a major role in the virulence and pathogenicity of this microbial pathogen. We selected the most soluble and compact ACP fragment (2042-2188), identified by genetic selection of in-frame fragments from random library experiments, to monitor the transfer of the P-pant moiety from Coenzyme A onto a conserved serine residue of this ACP domain.
Selection and orientation of different particles in single particle imaging.
Venue: Journal of structural biology

The short pulses of X-ray free electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. The particles are injected into the beam in random orientations and they should be identical. However, in real experimental conditions it is not always possible to have identical particles. In this paper we show that the correlation maximization method, developed earlier, is able to select identical particles from a mixture and find their orientations simultaneously.
Modular peptide binding: from a comparison of natural binders to designed armadillo repeat proteins.
Venue: Journal of structural biology

Several binding scaffolds that are not based on immunoglobulins have been designed as alternatives to traditional monoclonal antibodies. Many of them have been developed to bind to folded proteins, yet cellular networks for signaling and protein trafficking often depend on binding to unfolded regions of proteins. This type of binding can thus be well described as a peptide-protein interaction. In this review, we compare different peptide-binding scaffolds, highlighting that armadillo repeat proteins (ArmRP) offer an attractive modular system, as they bind a stretch of extended peptide in a repeat-wise manner. Instead of generating each new binding molecule by an independent selection, preselected repeats - each complementary to a piece of the target peptide - could be designed and assembled on demand into a new protein, which then binds the prescribed complete peptide. Stacked armadillo repeats (ArmR), each typically consisting of 42 amino acids arranged in three α-helices, build an elongated superhelical structure which enables binding of peptides in extended conformation. A consensus-based design approach, complemented with molecular dynamics simulations and rational engineering, resulted in well-expressed monomeric proteins with high stability. Peptide binders were selected and several structures were determined, forming the basis for the future development of modular peptide-binding scaffolds.