nils-herrmann/clean_scirepeval huggingface dataset:
The guanine nucleotide exchange factor Rlf interacts with SH3 domain-containing proteins via a binding site with a preselected conformation.
Venue: Journal of structural biology

Rlf is a guanine nucleotide exchange factor for the small G-proteins RalA and RalB and couples Ras- to Ral-signalling. Here the crystal structure of the catalytic module of Rlf consisting of a REM- and a CDC25-homology domain is determined. The structure is distinguished by an extended three stranded β-sheet called the flagpole. The flagpole is a conserved element in the RalGDS family of guanine nucleotide exchange factors and stabilises the orientation of the REM-domain relative to the CDC25-homology domain. A proline-rich sequence in the flagpole is unique to Rlf and several proteins that interact with this sequence by SH3 domains are identified. Conformational pre-selection results in a gain of affinity and contributes to the establishment of SH3 domain selectivity.
Three-dimensional reconstruction of icosahedral particles from single micrographs in real time at the microscope.
Venue: Journal of structural biology

Single particle analysis is a valuable tool in cryo-electron microscopy for determining the structure of biological complexes. However, the conformational state and the preparation of the sample are factors that play a critical role in the ultimate attainable resolution. In some cases extensive analysis at the microscope of a sample under different conditions is required to derive the optimal acquisition conditions. Currently this analysis is limited to raw micrographs, thus conveying only limited information on the structure of the complex. We are developing a computing system that generates a three-dimensional reconstruction from a single micrograph acquired under cryogenic and low dose conditions, and containing particles with icosahedral symmetry. The system provides the microscopist with immediate structural information from a sample while it is in the microscope and during the preliminary acquisition stage. The system is designed to run without user intervention on a multi-processor computing resource and integrates all the processing steps required for the analysis. Tests performed on experimental data sets show that the probability of obtaining a reliable reconstruction from one micrograph is primarily determined by the quality of the sample, with success rates close to 100% when sample conditions are optimal, and decreasing to about 60% when conditions are sub-optimal. The time required to generate a reconstruction depends significantly on the diameter of the particles, and in most instances takes about 1min. The proposed approach can provide valuable three-dimensional information, albeit at low resolution, on conformational states, epitope binding, and stoichiometry of icosahedral multi-protein complexes.
Reduced HIV-1 integrase flexibility as a mechanism for raltegravir resistance.
Venue: Journal of structural biology

HIV-1 integrase is an essential enzyme necessary for the replication of the HIV virus as it catalyzes the insertion of the viral genome into the host chromosome. Raltegravir was the first integrase inhibitor approved by the FDA for antiretroviral treatment. HIV patients on raltegravir containing regimens often develop drug resistance mutations at residue 140 and 148 in the catalytic 140's loop resulting in a 5-10 fold decrease in susceptibility to raltegravir. Obtaining crystallographic structure information on the Q148H/R, G140S/A primary and secondary mutations has been elusive. Using 10 ns molecular dynamics simulations, we present a detailed analysis of the structural changes induced by these mutations. The formation frequency of a transient helix in the catalytic 140's loop is increased and the length of this helix is extended from 3-residues to 4 in the mutants relative to the wild type. This helix causes reduced flexibility in the protein active site and therefore serves as a gating mechanism restricting the access of raltegravir to the integrase binding pocket. These results suggest that resistance to raltegravir occurs through a common mechanism of altering the formation frequency of transient secondary structures such as α2 and β5 in addition to the conformational changes in the 140's loop therefore decreasing the flexibility of the HIV-1 integrase protein. The reduced integrase flexibility serves as a mechanism of resistance to raltegravir.
Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.
Venue: Journal of structural biology

We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.
Likelihood-based classification of cryo-EM images using FREALIGN.
Venue: Journal of structural biology

We describe an implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software. Particle alignment parameters are determined by maximizing a joint likelihood that can include hierarchical priors, while classification is performed by expectation maximization of a marginal likelihood. We test the FREALIGN implementation using a simulated dataset containing computer-generated projection images of three different 70S ribosome structures, as well as a publicly available dataset of 70S ribosomes. The results show that the mixed strategy of the new FREALIGN algorithm yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.
Femoral osteocyte lacunar density, volume and morphology in women across the lifespan.
Venue: Journal of structural biology

Osteocytes are believed to be the primary agents of mechanosensing in bone. Due to this important role in the structure-function relationship of bone, osteocytes and the spaces they occupy (lacunae) are of increasing interest. Changes in lacunae with age are of particular interest in women since they are more susceptible to bone loss and fragility associated with senescent diseases including osteoporosis. This study's purpose was to test whether differences exist in lacunar density (lacunae/mm(3) of bone), orientation and morphology in the cortex of adult women spanning the human lifespan. Anterior blocks from the femoral shaft from 30 women aged 20-86years were imaged by synchrotron-radiation micro-CT. No significant relation between lacunar density and age was detected. A significant reduction in lacunar volume with age (p<0.001) was observed, alongside changes in lacunar morphology. When divided into two groups (<50 and >50years) the younger group's lacunae were ∼30% larger and were flatter (p<0.001) and less equant (spherical) (p<0.001). To our knowledge the observation that lacunar volume and morphology change over the human lifespan is novel, potentially resulting from preferential surface infilling within the extracellular space. The functional impact of this infilling is unclear but such a change in scale likely impacts the mechanosensing function of the osteocyte network. Limitations in resolution prevented us from assessing if this infilling is associated with disruption of the canaliculi. This hypothesis warrants further investigation as, if confirmed, it would represent a profound negative impact on the osteocyte network and may provide new insights into age-related bone loss.
High-resolution scanning electron microscopy of the cytoskeleton of Tritrichomonas foetus.
Venue: Journal of structural biology

Tritrichomonas foetus is a pathogenic protozoan that causes bovine trichomoniasis. In addition to its importance in veterinary medicine, this parasite is also a good representative of one the earliest eukaryotic cells available for study. T. foetus contains organelles that are common to all eukaryotic cells as well as uncommon cell structures such as hydrogenosomes and a complex and elaborate cytoskeleton that constitutes the mastigont system. The mastigont system is mainly formed by several proteinaceous structures that are associated with basal bodies, the pelta-axostylar complex and the costa. Although the structural organization of trichomonad cytoskeletons has been analyzed using several techniques, observation using a new generation of scanning electron microscopes with a resolution of 0.8nm has allowed more detailed visualization of the three-dimensional organization of the mastigont system. Moreover, this study revealed the presence of new structures, such as the costa accessory filament, and the presence of two groups of microtubules that form the pelta-axostylar system.
Enhanced cellulose orientation analysis in complex model plant tissues.
Venue: Journal of structural biology

The orientation distribution of cellulose microfibrils in the plant cell wall is a key parameter for understanding anisotropic plant growth and mechanical behavior. However, precisely visualizing cellulose orientation in the plant cell wall has ever been a challenge due to the small size of the cellulose microfibrils and the complex network of polymers in the plant cell wall. X-ray diffraction is one of the most frequently used methods for analyzing cellulose orientation in single cells and plant tissues, but the interpretation of the diffraction images is complex. Traditionally, circular or square cells and Gaussian orientation of the cellulose microfibrils have been assumed to elucidate cellulose orientation from the diffraction images. However, the complex tissue structures of common model plant systems such as Arabidopsis or aspen (Populus) require a more sophisticated approach. We present an evaluation procedure which takes into account the precise cell geometry and is able to deal with complex microfibril orientation distributions. The evaluation procedure reveals the entire orientation distribution of the cellulose microfibrils, reflecting different orientations within the multi-layered cell wall. By analyzing aspen wood and Arabidopsis stems we demonstrate the versatility of this method and show that simplifying assumptions on geometry and orientation distributions can lead to errors in the calculated microfibril orientation pattern. The simulation routine is intended to be used as a valuable tool for nanostructural analysis of plant cell walls and is freely available from the authors on request.
Novel structural labeling method using cryo-electron tomography and biotin-streptavidin system.
Venue: Journal of structural biology

There are a number of large macromolecular complexes that play important roles in the cell, and identifying the positions of their components is a key step to understanding their structure and function. Several structural labeling methods have been applied to electron microscopy in order to locate a specific component within a macromolecular complex, but each method is associated with problems in specificity, occupancy, signal intensity or precision. Here, we report a novel method for identifying the 3D locations of proteins using biotin-streptavidin labeling and cryo-electron tomography. We labeled a biotinylation-tagged intermediate chain of an axonemal dynein by streptavidin within the Chlamydomonas axoneme and visualized the 3D positions of the labels using subtomogram averaging. Increase of the density attributed to the bound streptavidin was validated by Student's t-test. In conclusion, the combination of the biotin-streptavidin system and cryo-electron tomography is a powerful method to investigate the structure of large macromolecular complexes.
A novel method for high-pressure freezing of adherent cells for frozen hydrated sectioning and CEMOVIS.
Venue: Journal of structural biology

With the development of Cryo Electron Microscopy Of Vitreous Sections (CEMOVIS), imaging cells in a close to native state has become a reality. However with the commonly used carriers for high-pressure freezing and cryo-sectioning, adherent grown cells either need to be detached from their substrate. Here a new method is presented for high-pressure freezing adherent growing cells for frozen-hydrated sectioning and CEMOVIS. Cells are cultured on golden grids, containing a carbon coated Formvar film, and frozen on a membrane carrier which provides the grids with the structural support needed to withstand the strain of trimming and cryo-sectioning. This method was successfully tested for the two different types of high-pressure freezers, those using a pressure chamber (HPM010, EMHPF, Wohlwend Compact 01/02, HPM100) and those directly pressurizing the sample (EMPact series).
Identification and first insights into the structure and biosynthesis of chitin from the freshwater sponge Spongilla lacustris.
Venue: Journal of structural biology

This work demonstrates that chitin is an important structural component within the skeletal fibers of the freshwater sponge Spongilla lacustris. Using a variety of analytical techniques ((13)C solid state NMR, FT-IR, Raman, NEXAFS, ESI-MS, Morgan-Elson assay and Calcofluor White Staining); we show that this sponge chitin is much closer to α-chitin, known to be present in other animals, than to β-chitin. Genetic analysis confirmed the presence of chitin synthases, which are described for the first time in a sponge. The presence of chitin in both marine (demosponges and hexactinellids) and freshwater sponges indicates that this important structural biopolymer was already present in their common ancestor.
Rational design of a zinc phthalocyanine binding protein.
Venue: Journal of structural biology

Phthalocyanines have long been used as primary donor molecules in synthetic light-powered devices due to their superior properties when compared to natural light activated molecules such as chlorophylls. Their use in biological contexts, however, has been severely restricted due to their high degree of self-association, and its attendant photoquenching, in aqueous environments. To this end we report the rational redesign of a de novo four helix bundle di-heme binding protein into a heme and Zinc(II) phthalocyanine (ZnPc) dyad in which the ZnPc is electronically and photonically isolated. The redesign required transformation of the homodimeric protein into a single chain four helix bundle and the addition of a negatively charge sulfonate ion to the ZnPc macrocycle. To explore the role of topology on ZnPc binding two constructs were made and the resulting differences in affinity can be explained by steric interference of the newly added connecting loop. Singular binding of ZnPc was verified by absorption, fluorescence, and magnetic circular dichroism spectroscopy. The engineering guidelines determined here, which enable the simple insertion of a monomeric ZnPc binding site into an artificial helical bundle, are a robust starting point for the creation of functional photoactive nanodevices.
A dodecameric ring-like structure of the N0 domain of the type II secretin from enterotoxigenic Escherichia coli.
Venue: Journal of structural biology

In many bacteria, secretins from the type II secretion system (T2SS) function as outer membrane gated channels that enable passage of folded proteins from the periplasm into the extracellular milieu. Cryo-electron microscopy of the T2SS secretin GspD revealed previously the dodecameric cylindrical architecture of secretins, and crystal structures of periplasmic secretin domains showed a modular domain organization. However, no high-resolution experimental data has as yet been provided about how the entire T2SS secretin or its domains are organized in a cylindrical fashion. Here we present a crystal structure of the N0 domain of the T2SS secretin GspD from enterotoxigenic Escherichia coli containing a helix with 12 subunits per turn. The helix has an outer diameter of ∼125Å and a pitch of only 24Å which suggests a model of a cylindrical dodecameric N0 ring whose dimensions correspond with the cryo-electron microscopy map of Vibrio cholerae GspD. The N0 domain is known to interact with the HR domain of the inner membrane T2SS protein GspC. When the new N0 ring model is combined with the known N0·HR crystal structure, a dodecameric double-ring of twelve N0-HR heterodimers is obtained. In contrast, the previously observed compact N0-N1 GspD module is not compatible with the N0 ring. Interestingly, a N0-N1 T3SS homolog is compatible with forming a N0-N1 dodecameric ring, due to a different N0-vs-N1 orientation. This suggests that the dodecameric N0 ring is an important feature of T2SS secretins with periplasmic domains undergoing considerable motions during exoprotein translocation.
Single-cell lysis for visual analysis by electron microscopy.
Venue: Journal of structural biology

The stochastic nature of biological systems makes the study of individual cells a necessity in systems biology. Yet, handling and disruption of single cells and the analysis of the relatively low concentrations of their protein components still challenges available techniques. Transmission electron microscopy (TEM) allows for the analysis of proteins at the single-molecule level. Here, we present a system for single-cell lysis under light microscopy observation, followed by rapid uptake of the cell lysate. Eukaryotic cells were grown on conductively coated glass slides and observed by light microscopy. A custom-designed microcapillary electrode was used to target and lyse individual cells with electrical pulses. Nanoliter volumes were subsequently aspirated into the microcapillary and dispensed onto an electron microscopy grid for TEM inspection. We show, that the cell lysis and preparation method conserves protein structures well and is suitable for visual analysis by TEM.
Stress-vs-time signals allow the prediction of structurally catastrophic events during fracturing of immature cartilage and predetermine the biomechanical, biochemical, and structural impairment.
Venue: Journal of structural biology

Trauma-associated cartilage fractures occur in children and adolescents with clinically significant incidence. Several studies investigated biomechanical injury by compressive forces but the injury-related stress has not been investigated extensively. In this study, we hypothesized that the biomechanical stress occurring during compressive injury predetermines the biomechanical, biochemical, and structural consequences. We specifically investigated whether the stress-vs-time signal correlated with the injurious damage and may allow prediction of cartilage matrix fracturing.



Superficial and deeper zones disks (SZDs, DZDs; immature bovine cartilage) were biomechanically characterized, injured (50% compression, 100%/s strain-rate), and re-characterized. Correlations of the quantified functional, biochemical and histological damage with biomechanical parameters were zonally investigated.



Injured SZDs exhibited decreased dynamic stiffness (by 93.04±1.72%), unresolvable equilibrium moduli, structural damage (2.0±0.5 on a 5-point-damage-scale), and 1.78-fold increased sGAG loss. DZDs remained intact. Measured stress-vs-time-curves during injury displayed 4 distinct shapes, which correlated with histological damage (p<0.001), loss of dynamic stiffness and sGAG (p<0.05). Damage prediction in a blinded experiment using stress-vs-time grades was 100%-correct and sensitive to differentiate single/complex matrix disruptions. Correlations of the dissipated energy and maximum stress rise with the extent of biomechanical and biochemical damage reached significance when SZDs and DZDs were analyzed as zonal composites but not separately.



The biomechanical stress that occurs during compressive injury predetermines the biomechanical, biochemical, and structural consequences and, thus, the structural and functional damage during cartilage fracturing. A novel biomechanical method based on the interpretation of compressive yielding allows the accurate prediction of the extent of structural damage.
Oligomerization of DDR1 ECD affects receptor-ligand binding.
Venue: Journal of structural biology

Discoidin domain receptor 1 (DDR1) is a widely expressed receptor tyrosine kinase (RTK) which regulates cell differentiation, proliferation and migration and remodeling of the extracellular matrix. Collagen(s) are the only known ligand for DDR1. We have previously reported that collagen stimulation leads to oligomerization of the full length receptor. In this study we investigated the effect of oligomerization of the DDR1 extracellular domain (ECD) pre and post ligand binding. Solid phase binding assays showed that oligomers of recombinant DDR1-Fc bound more strongly to collagen compared to dimeric DDR1-Fc alone. In addition, DDR1-Fc itself could oligomerize upon in-vitro binding to collagen when examined using atomic force microscopy. Inhibition of dynamin mediated receptor endocytosis could prevent ligand induced endocytosis of DDR1b-YFP in live cells. However inhibition of receptor endocytosis did not affect DDR1 oligomerization. In summary our results demonstrate that DDR1 ECD plays a crucial role in receptor oligomerization which mediates high-affinity interactions with its ligand.
Crystal lattice tilting in prismatic calcite.
Venue: Journal of structural biology

We analyzed the calcitic prismatic layers in Atrina rigida (Ar), Haliotis iris (Hi), Haliotis laevigata (HL), Haliotis rufescens (Hrf), Mytilus californianus (Mc), Pinctada fucata (Pf), Pinctada margaritifera (Pm) shells, and the aragonitic prismatic layer in the Nautilus pompilius (Np) shell. Dramatic structural differences were observed across species, with 100-μm wide single-crystalline prisms in Hi, HL and Hrf, 1-μm wide needle-shaped calcite prisms in Mc, 1-μm wide spherulitic aragonite prisms in Np, 20-μm wide single-crystalline calcite prisms in Ar, and 20-μm wide polycrystalline calcite prisms in Pf and Pm. The calcite prisms in Pf and Pm are subdivided into sub-prismatic domains of orientations, and within each of these domains the calcite crystal lattice tilts gradually over long distances, on the order of 100 μm, with an angle spread of crystal orientation of 10-20°. Furthermore, prisms in Pf and Pm are harder than in any other calcite prisms analyzed, their nanoparticles are smaller, and the angle spread is strongly correlated with hardness in all shells that form calcitic prismatic layers. One can hypothesize a causal relationship of these correlated parameters: greater angle spread may confer greater hardness and resistance to wear, thus providing Pf and Pm with a structural advantage in their environment. This is the first structure-property relationship thus far hypothesized in mollusk shell prisms.