nils-herrmann/clean_scirepeval huggingface dataset:
The dimer formed by the periplasmic domain of EpsL from the Type 2 Secretion System of Vibrio parahaemolyticus.
Venue: Journal of structural biology

The Type 2 Secretion System (T2SS), occurring in many Gram-negative bacteria, is responsible for the transport of a diversity of proteins from the periplasm across the outer membrane into the extracellular space. In Vibrio cholerae, the T2SS secretes several unrelated proteins including the major virulence factor cholera toxin. The T2SS consists of three sub-assemblies, one of which is the Inner Membrane Complex which contains multiple copies of five proteins, including the bitopic membrane protein EpsL. Here, we report the 2.3A resolution crystal structure of the periplasmic domain of EpsL (peri-EpsL) from Vibrio parahaemolyticus, which is 56% identical in sequence to its homolog in V. cholerae. The domain adopts a circular permutation of the "common" ferredoxin fold with two contiguous sub-domains. Remarkably, this infrequently occurring permutation was for the first time observed in the periplasmic domain of EpsM (peri-EpsM), another T2SS protein which interacts with EpsL. These two domains are 18% identical in sequence which may indicate a common evolutionary origin. Both peri-EpsL and peri-EpsM form dimers, but the organization of the subunits in these dimers appears to be entirely different. We have previously shown that the cytoplasmic domain of EpsL is also dimeric and forms a heterotetramer with the first domain of the "secretion ATPase" EpsE. The latter enzyme is most likely hexameric. The possible consequences of the combination of the different symmetries of EpsE and EpsL for the architecture of the T2SS are discussed.
Phosphorylation and the N-terminal extension of the regulatory light chain help orient and align the myosin heads in Drosophila flight muscle.
Venue: Journal of structural biology

X-ray diffraction of the indirect flight muscle (IFM) in living Drosophila at rest and electron microscopy of intact and glycerinated IFM was used to compare the effects of mutations in the regulatory light chain (RLC) on sarcomeric structure. Truncation of the RLC N-terminal extension (Dmlc2(Delta2-46)) or disruption of the phosphorylation sites by substituting alanines (Dmlc2(S66A, S67A)) decreased the equatorial intensity ratio (I(20)/I(10)), indicating decreased myosin mass associated with the thin filaments. Phosphorylation site disruption (Dmlc2(S66A, S67A)), but not N-terminal extension truncation (Dmlc2(Delta2-46)), decreased the 14.5nm reflection intensity, indicating a spread of the axial distribution of the myosin heads. The arrangement of thick filaments and myosin heads in electron micrographs of the phosphorylation mutant (Dmlc2(S66A, S67A)) appeared normal in the relaxed and rigor states, but when calcium activated, fewer myosin heads formed cross-bridges. In transgenic flies with both alterations to the RLC (Dmlc2(Delta2-46; S66A, S67A)), the effects of the dual mutation were additive. The results suggest that the RLC N-terminal extension serves as a "tether" to help pre-position the myosin heads for attachment to actin, while phosphorylation of the RLC promotes head orientations that allow optimal interactions with the thin filament.
Relevance of metal ions for lipase stability: structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion.
Venue: Journal of structural biology

We have studied the accessibility of the structural calcium ion in the Burkholderia glumae lipase and the consequences of its removal on the protein conformation by different biophysical techniques (circular dichroism, fluorimetry, and mass spectrometry) and by molecular-dynamics simulations. We show that, in the native protein, calcium is not accessible unless specific flexible loops are displaced, for example, by a temperature increase. Such movements concern the whole calcium-binding pocket and particularly the environment of the coordinating aspartate residue 241. As a consequence of metal depletion the protein unfolds irreversibly and undergoes aggregation. The removal of the metal ion causes major structural transitions and leads to an increase in beta-structure, in particular in protein regions that are largely unstructured in the native protein and encompass the calcium coordination residues.
Enamel dictates whole tooth deformation: a finite element model study validated by a metrology method.
Venue: Journal of structural biology

In order to understand whole tooth behavior under load the biomechanical role of enamel and dentin has to be determined. We approach this question by comparing the deformation pattern and stiffness of intact teeth under load with the deformation pattern and stiffness of the same teeth after the enamel has been mechanically compromised by introducing a defect. FE models of intact human premolars, based on high resolution micro-CT scans, were generated and validated by in vitro electronic speckle pattern interferometry (ESPI) experiments. Once a valid FE model was established, we exploit the flexibility of the FE model to gain more insight into whole tooth function. Results show that the enamel cap is an intrinsically stiff biological structure and its morphology dictates the way a whole tooth will mechanically behave under load. The mechanical properties of the enamel cap were sufficient to mechanically maintain almost its entire stiffness function under load even when a small defect (cavity simulating caries) was introduced into its structure and breached the crown integrity. We conclude that for the most part, that enamel and not dentin dictates the mechanical behavior of the whole tooth.
Ultrastructure and mineral distribution in the tergal cuticle of the terrestrial isopod Titanethes albus. Adaptations to a karst cave biotope.
Venue: Journal of structural biology

Composition and spatial distribution of organic and inorganic materials within the cuticle of isopods vary between species. These variations are related to the behaviour and habitat of the animal. The troglobiotic isopod Titanethes albus lives in the complete darkness of caves in the Slovenian Karst. This habitat provides constant temperature and saturated humidity throughout the year and inconsistent food supply. These conditions should have lead to functional adaptations of arthropod cuticles. However, studies on structure and composition of cave arthropod cuticles are rare and lacking for terrestrial isopods. We therefore analysed the tergite cuticle of T. albus using transmission and field-emission electron microscopy, confocal micro-Raman spectroscopic imaging, quantitative X-ray diffractometry, thermogravimetric analysis and atomic absorption spectroscopy. The ultrastructure of the epicuticle suggests a poor resistance against water loss. A weak interconnection between the organic and mineral phase within the endo- and exocuticle, a comparatively thin apical calcite layer, and almost lack of magnesium within the calcite crystal lattice suggest that the mechanical strength of the cuticle is low in the cave isopod. This may possibly be of advantage in maintaining high cuticle flexibility and reducing metabolic expenditures.
Assembly of Kch, a putative potassium channel from Escherichia coli.
Venue: Journal of structural biology

Attempts to explore the structure and function of Kch, a putative potassium channel of Escherichia coli have yielded varying results; potassium-associated functions have been found in vivo but not in vitro. Here the kch gene is shown to produce two proteins, full-length Kch and the large C-terminal cytosolic domain (the RCK domain). Further, these two proteins are associated at the initial stages of purification. Previous structural studies of full-length Kch claim that the isolated protein forms large aggregates that are not suitable for analysis. The results presented here show that the purified protein sample, although heterogeneous, has one major population with a mass of about 400kDa, implying the presence of two Kch tetramers in a complex form. A three dimensional reconstruction at 25A based on electron microscopy data from negatively stained particles, revealed a 210A long and 95A wide complex in which the two tetrameric Kch units are linked by their RCK domains, giving rise to a large central ring of density. The formation of this dimer of tetramers on expression or during purification, may explain why attempts to reconstitute Kch into liposomes for activity measurements have failed.
Three-dimensional structure of the detergent-solubilized Vibrio cholerae cytolysin (VCC) heptamer by electron cryomicroscopy.
Venue: Journal of structural biology

Vibrio cholerae cytolysin (VCC) is a pore-forming toxin that inserts a lytic water-filled channel into susceptible host membranes. Assembly of the toxin on cell surfaces may be enhanced by two tandem lectin domains, in addition to direct interactions with lipids and cholesterol within the membrane itself. We used single-particle electron cryomicroscopy (cryoEM) to generate a low-resolution molecular structure of the detergent-solubilized VCC oligomer to 20A resolution. After confirming a heptameric arrangement of individual protomers, sevenfold averaging around the central pore was utilized to improve the structure. Docking of the previously determined VCC protoxin crystal structure was possible with rigid-body rearrangements between the cytolytic and lectin domains. A second cryoEM reconstruction of a truncated VCC mutant supported the topology of our model in which the carboxyl-terminal lectin domain forms "spikes" around the toxin core with the putative carbohydrate receptor-binding site accessible on the surface of the oligomer. This finding points to an assembly mechanism in which lectin domains may remain bound to receptors on the cell surface throughout assembly of the cytolytic toxin core and explains the hemagglutinating activity of purified toxin. Our model provides an insight into the structural rearrangements that accompany VCC-mediated cytolysis and may aid in the engineering of novel pore-forming toxins to attack specific cells towards therapeutic ends.
Cryo-X-ray tomography of vaccinia virus membranes and inner compartments.
Venue: Journal of structural biology

Vitrified unstained purified vaccinia virus particles have been used as a test sample to evaluate the capabilities of cryo-X-ray tomography. Embedded in a thick layer of vitreous ice, the viral particles representing the mature form of the virus (MV) were visualized using full-field transmission X-ray tomography. The tomographic reconstructions reveal the viral brick-shaped characteristic structures with a size of 250x270x360nm(3). The X-ray tomograms show the presence of a clearly defined external envelope, together with an inner core surrounded by an internal envelope, including areas with clear differential density, which correlate well with those features previously described for these viral particles using electron microscopy analyses. A quantitative assessment of the resolution attained in X-ray and electron tomograms of the viral particles prepared under the same conditions yields values of 25.7 and 6.7nm half-pitch, respectively. Although the resolution of the X-ray microscope is well above the dimensions of the membranous compartments, the strong differential contrast exhibited makes it possible to precisely reveal them without any contrasting reagent within this small and complex biological sample.
Structure and function of the l-threonine dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis.
Venue: Journal of structural biology

The X-ray structure of the holo-form of l-threonine dehydrogenase (TDH) from Thermococcus kodakaraensis (TkTDH) has been determined at 2.4A resolution. TDH catalyses the NAD(+)-dependent oxidation of l-threonine to 2-amino-3-ketobutyrate, and is one of the first enzymes in this family to be solved by X-ray crystallography. The enzyme is a homo-tetramer, each monomer consisting of 350 amino acids that form two domains; a catalytic domain and a nicotinamide co-factor (NAD(+))-binding domain, which contains an alpha/beta Rossmann fold motif. An extended twelve-stranded beta-sheet is formed by the association of pairs of monomers in the tetramer. TkTDH shows strong overall structural similarity to TDHs from thermophiles and alcohol dehydrogenases (ADH) from lower life forms, despite low sequence homology, exhibiting the same overall fold of the monomer and assembly of the tetramer. The structure reveals the binding site of the essential co-factor NAD(+) which is present in all subunits. Docking studies suggest a mode of interaction of TDH with 2-amino-3-ketobutyrate CoA ligase, the subsequent enzyme in the pathway for conversion of threonine to glycine. TDH is known to form a stable functional complex with 2-amino-3-ketobutyrate ligase, most probably to shield an unstable intermediate.
Structure of first- and second-stage mineralized elements in teeth of the sea urchin Lytechinus variegatus.
Venue: Journal of structural biology

Microstructure of the teeth of the sea urchin Lytechinus variegatus was investigated using optical microscopy, SEM (scanning electron microscopy) and SIMS (secondary ion mass spectroscopy). The study focused on the internal structure of the first-stage mineral structures of high Mg calcite (primary, secondary and carinar process plates, prisms) and on morphology of the columns of second-stage mineral (very high Mg calcite) that cement the first-stage material together. Optical micrographs under polarized light revealed contrast in the centers (midlines) of carinar process plates and in prisms in polished sections; staining of primary and carinar process plates revealed significant dye uptake at the plate centers. Demineralization with and without fixation revealed that the midlines of primary and carinar process plates (but not secondary plates) and the centers of prisms differed from the rest of the plate or prism, and SIMS showed proteins concentrated in these plate centers. SEM was used to study the morphology of columns, the fracture surfaces of mature teeth and the 3D morphology of prisms. These observations of internal structures in plates and prisms offer new insight into the mineralization process and suggest an important role for protein inclusions within the first-stage mineral. Some of the 3D structures not reported previously, such as twisted prisms and stacks of carinar process plates with nested wrinkles, may represent structural strengthening strategies.
Synthesis and antimicrobial activity of truncated fragments and analogs of citropin 1.1: The solution structure of the SDS micelle-bound citropin-like peptides.
Venue: Journal of structural biology

Citropin 1.1 is a basic, highly hydrophobic, 16-amino acid peptide (GLFDVIKKVASVIGGL-NH(2)), displaying wide-spectrum antimicrobial activities. In this paper we describe the synthesis and antimicrobial properties of citropin 1.1 and its 18 analogs constituting mostly truncated fragments of citropin 1.1. Moreover, we examined conformational properties of citropin 1.1 and its two analogs, (1-12)citropin and (1-13)[Ala(4)]citropin, using FTIR, CD and NMR spectroscopies. Three-dimensional structures of the peptides were determined using molecular dynamics (MD) simulations with time-averaged (TAV) restraints obtained from NMR spectra measured in micellar concentration of sodium dodecyl sulfate (SDS). Earlier investigations showed that in TFE solution, citropin 1.1 is a single helix all along the backbone. However, this structure is not retained in the presence of SDS micelle. In H(2)O/SDS-d(25) solution, citropin 1.1 adopts two alpha-helices in the fragments 4-7 and 10-16, respectively, separated by betaIV-turn at position 8, 9. The (1-12)citropin adopts an alpha-helical structure along the entire backbone. In turn, (1-13)[Ala(4)]citropin demonstrates the tendency to adopt only a short alpha-helix in the middle part. Moreover, the conversion of alpha-helix to 3(10)-helix has been noticed in about 30% of conformations. The 3(10)-helical units could be thermodynamic intermediates during folding and unfolding of the alpha-helical segment of the peptide.
Microtexture of larval shell of oyster, Crassostrea nippona: a FIB-TEM study.
Venue: Journal of structural biology

The initial formation and subsequent development of larval shells in marine bivalve, Crassostrea nippona were investigated using the FIB-TEM technique. Fourteen hours after fertilization (the trochophore stage), larvae form an incipient shell of 100-150nm thick with a columnar contrast. Selected-area electron diffraction analysis showed a single-crystal aragonite pattern with the c-axis perpendicular to the shell surface. Plan-view TEM analysis suggested that the shell contains high density of {110} twins, which are the origin of the columnar contrast in the cross-sectional images. 72h after fertilization (the veliger stage), the shell grows up to 1.2-1.4mum thick accompanying an additional granular layer between the preexisting layer and embryo to form a distinctive two-layer structure. The granular layer is also composed of aragonite crystals sharing their c-axes perpendicular to the shell surface, but the crystals are arranged with a flexible rotation around the c-axes and not restricted solely to the {110} twin relation. No evidence to suggest the existence of amorphous calcium carbonate (ACC) was found through the observation. The well-regulated crystallographic properties found in the present sample imply initial shell formation probably via a direct deposition of crystalline aragonite.
Structure/function studies on two type 1 ribosome inactivating proteins: Bouganin and lychnin.
Venue: Journal of structural biology

The three-dimensional structures of two type 1 RIPs, bouganin and lychnin, has been solved. Their adenine polynucleotide glycosylase activity was also determined together with other known RIPs: dianthin 30, PAP-R, momordin I, ricin A chain and saporin-S6. Saporin-S6 releases the highest number of adenine molecules from rat ribosomes, and poly(A), while its efficiency is similar to dianthin 30, bouganin and PAP-R on herring sperm DNA. Measures of the protein synthesis inhibitory activity confirmed that saporin-S6 is the most active. The overall structure of bouganin and lychnin is similar to the other considered RIPs and the typical RIP fold is conserved. The superimpositioning of their C(alpha) atoms highlights some differences in the N-terminal and C-terminal domains. A detailed structural analysis indicates that the efficiency of saporin-S6 on various polynucleotides can be ascribed to a negative electrostatic surface potential at the active site and several exposed positively charged residues in the region around that site. These two conditions, not present at the same time in other examined RIPs, could guarantee an efficient interaction with the substrate and an efficient catalysis.
Pioneer cells established by the [SWI+] prion can promote dispersal and out-crossing in yeast
Venue: PLoS biology

To thrive in an ever-changing environment, microbes must widely distribute their progeny to colonize new territory. Simultaneously, they must evolve and adapt to the stresses of unpredictable surroundings. In both of these regards, diversity is key—if an entire population moved together or responded to the environment in the same way, it could easily go extinct. Here, we show that the epigenetic prion switch [SWI+] establishes a specialized subpopulation with a “pioneer” phenotypic program in Saccharomyces cerevisiae. Cells in the pioneer state readily disperse in water, enabling them to migrate and colonize new territory. Pioneers are also more likely to find and mate with genetically diverse partners, as inhibited mating-type switching causes mother cells to shun their own daughters. In the nonprion [swi−] state, cells instead have a “settler” phenotype, forming protective flocs and tending to remain in their current position. Settler cells are better able to withstand harsh conditions like drought and alkaline pH. We propose that these laboratory observations reveal a strategy employed in the wild to rapidly diversify and grant distinct, useful roles to cellular subpopulations that benefit the population as a whole.
The poverty-related neglected diseases: Why basic research matters
Venue: PLoS biology

Together, malaria and the neglected tropical diseases (NTDs) kill more than 800,000 people annually, while creating long-term disability in millions more. International support for mass drug administration, bed nets, and other preventive measures has resulted in huge public health gains, while support for translational research is leading to the development of some new neglected disease drugs, diagnostics, and vaccines. However, funding for basic science research has not kept up, such that we are missing opportunities to create a more innovative pipeline of control tools for parasitic and related diseases. There is an urgent need to expand basic science approaches for neglected diseases, especially in the areas of systems biology and immunology; ecology, evolution, and mathematical biology; functional and comparative OMICs; gene editing; expanded use of model organisms; and a new single-cell combinatorial indexing RNA sequencing approach. The world’s poor deserve access to innovation for neglected diseases. It should be considered a fundamental human right.
Capacity of tTreg generation is not impaired in the atrophied thymus
Venue: PLoS biology

Postnatal thymic epithelial cell (TEC) homeostatic defect- or natural aging-induced thymic atrophy results in a decline in central T-cell tolerance establishment, which is constituted by thymocyte negative selection and cluster of differentiation (CD) 4+ thymic regulatory T (tTreg) cell generation. Emerging evidence shows this decline mainly results from defects in negative selection, but there is insufficient evidence regarding whether tTreg cell generation is also impaired. We mechanistically studied tTreg cell generation in the atrophied thymus by utilizing both postnatal TEC-defective (resulting from FoxN1-floxed conditional knockout [cKO]) and naturally aged mouse models. We found that the capacity of tTreg cell generation was not impaired compared to CD4+ thymic conventional T cells, suggesting thymic atrophy positively influences tTreg cell generation. This is potentially attributed to decreased T cell receptor (TCR) signaling strength due to inefficiency in promiscuous expression of self-antigens or presenting a neo-self-antigen by medullary TECs, displaying decreased negative selection-related marker genes (Nur77 and CD5high) in CD4 single positive (SP) thymocytes. Our results provide evidence that the atrophied thymus attempts to balance the defective negative selection by enhancing tTreg cell generation to maintain central T-cell tolerance in the elderly. Once the balance is broken, age-related diseases could take place.