nils-herrmann/clean_scirepeval huggingface dataset:
Carotenoids in nestling Montagu’s harriers: variations according to age, sex, body condition and evidence for diet-related limitations
Venue: Journal of Comparative Physiology B

Carotenoids are colored pigments forming the basis of many avian social traits. Before their utilization carotenoids must be acquired through diet and mobilized for specific uses. The relationships between carotenoid-based coloration, circulating carotenoids and body condition have been well studied in adult birds, but little is known in nestlings. Here, we investigated variations in carotenoid-based coloration in a raptor nestling, the Montagu’s harrier (Circus pygargus), both in captivity and in natural conditions, and within a vole (poor-carotenoid source and cyclic prey) specialist population. We studied these variations according to nestling age and sex, and possible limitations in carotenoid availability by comparing years of contrasted prey abundance and using carotenoid supplementation experiments. Captive nestlings, fed only with mice, were strongly carotenoid limited. Wild nestlings were also carotenoid limited, especially in a year of high vole abundance. Nestlings were in better condition but less colored during a peak vole abundance year than during a low vole abundance year, when harriers targeted more alternative preys (birds, insects). Thus, variation in vole abundance resulted in a de-coupling of body condition and carotenoid-based coloration in this population. This suggested that the positive relation between the body condition and carotenoid-based traits, typically found in adult birds, could be restricted to adults or nestlings of species that feed on carotenoid-rich food. Our results should stimulate more work on the functions and mechanisms of carotenoid-based traits in nestlings, which deserve more attention and most likely differ from those of adult birds.
Correlation of the amino-acid sequence and the 3D structure of the functional domain of EmaA from Aggregatibacter actinomycetemcomitans.
Venue: Journal of structural biology

Adhesion to collagen is an important virulence determinant for the periodontal pathogen Aggregatibacter actinomycetemcomitans. Binding to collagen is mediated by the extracellular-matrix protein adhesin-A (EmaA). EmaA is a homotrimeric autotransporter protein that forms flexible antenna-like appendages on the bacterium surface. An ellipsoidal structure at the distal end of the appendage, composed of three subdomains, contains the functional domain of the molecule. A correlation between amino-acid sequence and subdomain structure (SI and SII) was proposed based on an analysis of the volume/molecular weight ratio. EmaA from three mutant strains (deletions of amino-acids 70-206 and 70-386 and a substitution mutation G162S) has been studied by electron microscopy to test this hypothesis. 3D structures were analyzed using single-axis tilt tomography of negatively stained preparations of bacteria combined with subvolume averaging. Additionally, a large number of 2D images of the apical domain of the adhesins from the mutants were extracted from micrographs of the bacterial surface, aligned and classified. The combined data showed that amino-acids 70-206 localize to subdomain SI and 70-386 comprise subdomains SI and SII. Moreover, we showed that the substitution mutation G162S, which abolishes collagen binding activity, does not affect the overall structural integrity of the functional domain. However, the structure of subdomain SI in this mutant is slightly altered with respect to the wild-type strain. These data also have allowed us to interpret the architectural features of each subdomain of EmaA in more detail and to correlate the 3D structure of the functional domain of EmaA with the amino-acid sequence.
Modeling chondrocyte patterns by elliptical cluster processes.
Venue: Journal of structural biology

Superficial zone chondrocytes (CHs) of human joints are spatially organized in distinct horizontal patterns. Among other factors, the type of spatial CH organization within a given articular surface depends on whether the cartilage has been derived from an intact joint or the joint is affected by osteoarthritis (OA). Furthermore, specific variations of the type of spatial organization are associated with particular states of OA. This association may prove relevant for early disease recognition based on a quantitative structural characterization of CH patterns. Therefore, we present a point process model describing the distinct morphology of CH patterns within the articular surface of intact human cartilage. This reference model for intact CH organization can be seen as a first step towards a model-based statistical diagnostic tool. Model parameters are fitted to fluorescence microscopy data by a novel statistical methodology utilizing tools from cluster and principal component analysis. This way, the complex morphology of surface CH patters is represented by a relatively small number of model parameters. We validate the point process model by comparing biologically relevant structural characteristics between the fitted model and data derived from photomicrographs of the human articular surface using techniques from spatial statistics.
Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure.
Venue: Journal of structural biology

MCPH1 is especially important for linking chromatin remodeling to DNA damage response. It contains three BRCT (BRCA1-carboxyl terminal) domains. The N-terminal region directly binds with chromatin remodeling complex SWI-SNF, and the C-terminal BRCT2-BRCT3 domains (tandem BRCT domains) are involved in cellular DNA damage response. The MCPH1 gene associates with evolution of brain size, and its variation can cause primary microcephaly. In this study we solve the crystal structures of MCPH1 natural variant (A761) C-terminal tandem BRCT domains alone as well as in complex with γH2AX tail. Compared with other structures of tandem BRCT domains, the most significant differences lie in phosphopeptide binding pocket. Additionally, fluorescence polarization assays demonstrate that MCPH1 tandem BRCT domains show a binding selectivity on pSer +3 and prefer to bind phosphopeptide with free COOH-terminus. Taken together, our research provides new structural insights into BRCT-phosphopeptide recognition mechanism.
Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitro.
Venue: Journal of structural biology

In this study, electron tomograms of plunge-frozen isolated chromatin in both open and compacted form were recorded. We have resolved individual nucleosomes in these tomograms in order to provide a 3D view of the arrangement of nucleosomes within chromatin fibers at different compaction states. With an optimized template matching procedure we obtained accurate positions and orientations of nucleosomes in open chromatin in "low-salt" conditions (5 mM NaCl). The mean value of the planar angle between three consecutive nucleosomes is 70°, and the mean center-to-center distance between consecutive nucleosomes is 22.3 nm. Since the template matching approach was not effective in crowded conditions, for nucleosome detection in compact fibers (40 mM NaCl and 1 mM MgCl(2)) we developed the nucleosome detection procedure based on the watershed algorithm, followed by sub-tomogram alignment, averaging, and classification by Principal Components Analysis. We find that in compact chromatin the nucleosomes are arranged with a predominant face-to-face stacking organization, which has not been previously shown for native isolated chromatin. Although the path of the DNA cannot be directly seen in compact conditions, it is evident that the nucleosomes stack with their dyad axis aligned in forming a "double track" conformation which is a consequence of DNA joining adjacent nucleosome stacks. Our data suggests that nucleosome stacking is an important mechanism for generating chromatin compaction in vivo.
Analysis of the yeast nucleoporin Nup188 reveals a conserved S-like structure with similarity to karyopherins.
Venue: Journal of structural biology

Nuclear pore complexes (NPCs) embedded in the double nuclear membrane mediate the entire nucleocytoplasmic transport between the nucleus and cytoplasm. Each NPC is composed of about 30 different proteins (nucleoporins or Nups), which exist in multiple (8, 16 or 32) copies within the NPC scaffold. Recently, we have identified and characterized the large structural Nups, Nup188 and Nup192, from the thermophilic eukaryote Chaetomium thermophilum, which exhibited superior properties for biochemical and structural studies, when compared to their mesophilic orthologs. Here, we study the large structural Nups from the model organism yeast Saccharomyces cerevisiae. Our data show that yeast Nup188 like its thermophilic orthologue ctNup188 exhibits a twisted S-like structure, which flexibly binds the linker nucleoporin Nic96 via a short conserved α-helix motif. Using bioinformatic methods, we have generated a pseudo-atomic structural model of Nup188 and its related Nup192, which further strengthens the view that the large α-solenoid structural Nups are related to karyopherins.
Tooth movements are guided by specific contact areas between the tooth root and the jaw bone: A dynamic 3D microCT study of the rat molar.
Venue: Journal of structural biology

Teeth sustain high loads over a lifetime and yet intact tooth failure is rare. The different structures of the tooth, jaw bone and the intervening soft periodontal ligament enable the tooth to endure repeated loading during mastication. Although mechanical and functional properties of the different components are thoroughly investigated, the manner in which the whole tooth functions under load is still enigmatic. A custom-made loading system inside a microCT scanner was used to directly visualize the root movements in relation to the jaw bone as the rat molar tooth was loaded. At low loads no contact was observed between the root surface and the bone, whereas at higher loads three specific contact areas between the root surface and the jaw bone were observed. These contact areas restrict tooth movement in the buccal-lingual direction, but enable the tooth to rock in a "seesaw" like manner in the distal-mesial direction. The contact areas appear to play a role in determining tooth motion and in turn define the manner in which the whole tooth moves when loaded. These observations are important for understanding basic structure-function relations of the tooth-PDL-bone system, and have direct implications for better understanding pathological and therapeutic processes in orthodontics, periodontics and jaw bone regeneration.
Nuclear lamina at the crossroads of the cytoplasm and nucleus.
Venue: Journal of structural biology

The nuclear lamina is a protein meshwork that lines the nuclear envelope in metazoan cells. It is composed largely of a polymeric assembly of lamins, which comprise a distinct sequence homology class of the intermediate filament protein family. On the basis of its structural properties, the lamina originally was proposed to provide scaffolding for the nuclear envelope and to promote anchoring of chromatin and nuclear pore complexes at the nuclear surface. This viewpoint has expanded greatly during the past 25 years, with a host of surprising new insights on lamina structure, molecular composition and functional attributes. It has been established that the self-assembly properties of lamins are very similar to those of cytoplasmic intermediate filament proteins, and that the lamin polymer is physically associated with components of the cytoplasmic cytoskeleton and with a multitude of chromatin and inner nuclear membrane proteins. Cumulative evidence points to an important role for the lamina in regulating signaling and gene activity, and in mechanically coupling the cytoplasmic cytoskeleton to the nucleus. The significance of the lamina has been vaulted to the forefront by the discovery that mutations in lamins and lamina-associated polypeptides lead to an array of human diseases. A key future challenge is to understand how the lamina integrates pathways for mechanics and signaling at the molecular level. Understanding the structure of the lamina from the atomic to supramolecular levels will be essential for achieving this goal.
Inroads into the structure and function of intermediate filament networks.
Venue: Journal of structural biology

Although intermediate filaments are one of three major cytoskeletal systems of vertebrate cells, they remain the least understood with respect to their structure and function. This is due in part to the fact that they are encoded by a large gene family which is developmentally regulated in a cell and tissue type specific fashion. This article is in honor of Ueli Aebi. It highlights the studies on IF that have been carried out by our laboratory for more than 40 years. Many of our advances in understanding IF are based on conversations with Ueli which have taken place during adventurous and sometimes dangerous hiking and biking trips throughout the world.
Zernike phase contrast cryo-electron tomography of whole mounted frozen cells.
Venue: Journal of structural biology

Cryo-electron tomography of frozen hydrated cells has provided cell biologists with an indispensable tool for delineating three-dimensional arrangements of cellular ultrastructure. To avoid the damage induced by electron irradiation, images of frozen hydrated biological specimens are generally acquired under low-dose conditions, resulting in weakly contrasted images that are difficult to interpret, and in which ultrastructural details remain ambiguous. Zernike phase contrast transmission electron microscopy can improve contrast, and can also fix a fatal problem related to the inherent low contrast of conventional electron microscopy, namely, image modulation due to the unavoidable setting of deep defocus. In this study, we applied cryo-electron tomography enhanced with a Zernike phase plate, which avoids image modulation by allowing in-focus setting. The Zernike phase contrast cryo-electron tomography has a potential to suppress grainy background generation. Due to the smoother background in comparison with defocus phase contrast cryo-electron tomography, Zernike phase contrast cryo-electron tomography could yield higher visibility for particulate or filamentous ultrastructure inside the cells, and allowed us to clearly recognize membrane protein structures.
Laboratory cryo soft X-ray microscopy.
Venue: Journal of structural biology

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.
Stabilization of vimentin coil2 fragment via an engineered disulfide.
Venue: Journal of structural biology

Cytoskeletal intermediate filaments (IFs) assemble from the elementary dimers based on a segmented α-helical coiled-coil (CC) structure. Crystallographic studies of IF protein fragments remain the main route to access their atomic structure. To enable crystallization, such fragments must be sufficiently short. As a consequence, they often fail to assemble into the correct CC dimers. In particular, human vimentin fragment D3 corresponding to the first half of coil2 (residues 261-335) stays monomeric in solution. We have induced its dimerization via introducing a disulfide link between two cysteines engineered in the hydrophobic core of the CC close to its N-terminus. The 2.3 Å crystal structure of the D3st (stabilized) fragment reveals a mostly parallel α-helical bundle structure in its N-terminal half which smoothly continues into a left-handed CC towards the C-terminus. This provides a direct evidence for a continuously α-helical structure of the coil2 segment and disproves the previously suggested existence of linker L2 separating it into two left-handed CCs. The general principles of CC dimer stabilization by disulfide introduction are also discussed.
From skeletal muscle to cancer: insights learned elucidating the function of tropomyosin.
Venue: Journal of structural biology

The tropomyosins (Tms) are a family of actin filament binding proteins that possess a simple dimeric α-helical coiled-coil structure along their entire length. Our knowledge of Tm structure and function has greatly expanded since they were first discovered in skeletal muscle almost 65 years ago. In multicellular organisms they exhibit extensive cell type specific isoform diversity. In this essay we discuss the genetic mechanisms by which this diversity is generated and its significance to actin-based cellular functions.
Interaction of mammalian end binding proteins with CAP-Gly domains of CLIP-170 and p150(glued).
Venue: Journal of structural biology

End binding proteins (EBs) track growing microtubule ends and play a master role in organizing dynamic protein networks. Mammalian cells express up to three different EBs (EB1, EB2, and EB3). Besides forming homodimers, EB1 and EB3 also assemble into heterodimers. One group of EB-binding partners encompasses proteins that harbor CAP-Gly domains. The binding properties of the different EBs towards CAP-Gly proteins have not been systematically investigated. This information is, however, important to compare and contrast functional differences. Here we analyzed the interactions between CLIP-170 and p150(glued) CAP-Gly domains with the three EB homodimers and the EB1-EB3 heterodimer. Using isothermal titration calorimetry we observed that some EBs bind to the individual CAP-Gly domains with similar affinities while others interact with their targets with pronounced differences. We further found that the two types of CAP-Gly domains use alternative mechanisms to target the C-terminal domains of EBs. We succeeded to solve the crystal structure of a complex composed of a heterodimer of EB1 and EB3 C-termini together with the CAP-Gly domain of p150(glued). Together, our results provide mechanistic insights into the interaction properties of EBs and offer a molecular framework for the systematic investigation of their functional differences in cells.
Rotor architecture in the yeast and bovine F1-c-ring complexes of F-ATP synthase.
Venue: Journal of structural biology

The F(1)F(O)-ATP synthase is a rotary molecular nanomotor. F(1) is a chemical motor driven by ATP hydrolysis while F(O) is an electrical motor driven by the proton flow. The two stepping motors are mechanically coupled through a common rotary shaft. Up to now, the three available crystal structures of the F(1)c(10) sub-complex of the yeast F(1)F(O)-ATP synthase were isomorphous and then named yF(1)c(10)(I). In this crystal form, significant interactions of the c(10)-ring with the F(1)-head of neighboring molecules affected the overall conformation of the F(1)-c-ring complex. The symmetry axis of the F(1)-head and the inertia axis of the c-ring were tilted near the interface between the F(1)-central stalk and the c-ring rotor, resulting in an unbalanced machine. We have solved a new crystal form of the F(1)c(10) complex, named yF(1)c(10)(II), inhibited by adenylyl-imidodiphosphate (AMP-PNP) and dicyclohexylcarbodiimide (DCCD), at 6.5Å resolution in which the crystal packing has a weaker influence over the conformation of the F(1)-c-ring complex. yF(1)c(10)(II) provides a model of a more efficient generator. yF(1)c(10)(II) and bovine bF(1)c(8) structures share a common rotor architecture with the inertia center of the F(1)-stator close to the rotor axis.
The sensor region of the ubiquitous cytosolic sensor kinase, PdtaS, contains PAS and GAF domain sensing modules.
Venue: Journal of structural biology

Two-component systems, a sensor histidine kinase (HK) and a response regulator (RR), are ubiquitous signaling systems that allow prokaryotes to respond to external challenges. HKs normally have sensing modules and highly conserved cytosolic histidine kinase and ATPase domains. The interaction between the activated phosphohistidine and the cognate RR allows an external signal to be passed from the exterior of gram-positive bacteria (GPB) to the cytoplasm. Orthologs of the PdtaS/PdtaR regulatory system, found in most GPB phyla, are unusual in two respects. The HK is not membrane anchored, and the RR acts at the level of transcriptional antitermination. The structure of the complete sensor region of the cytosolic HK, PdtaS, from Mycobacterium tuberculosis consists of closely linked GAF and PAS domains. The structure and sequence analysis suggest that the PdtaS/PdtaR regulatory system is structurally equivalent to the EutW/EutV system regulating ethanolamine catabolism in some phyla but that the effector for the PAS domain is not ethanolamine in the Actinobacteria.
Optimizing the refolding conditions of self-assembling polypeptide nanoparticles that serve as repetitive antigen display systems
Venue: Journal of Structural Biology

Abstract
 
 Nanoparticles show great promise as potent vaccine candidates since they are readily taken up by the antigen presenting cells of the immune system. The particle size and the density of the B cell epitopes on the surface of the particles greatly influences the strength of the humoral immune response. We have developed a novel type of nanoparticle composed of peptide building blocks (Raman et al., 2006) and have used such particles to design vaccines against malaria and SARS (Kaba et al., 2009; Pimentel et al., 2009). Here we investigate the biophysical properties and the refolding conditions of a prototype of these self-assembling polypeptide nanoparticles (SAPNs). SAPNs are formed from a peptide containing a pentameric and a trimeric coiled-coil domain. At near physiological conditions the peptide self-assembles into about 27nm, roughly spherical SAPNs. The average size of the SAPNs increases with the salt concentration. The optimal pH for their formation is between 7.5 and 8.5, while aggregation occurs at lower and higher values. A glycerol concentration of about 5% v/v is required for the formation of SAPNs with regular spherical shapes. These studies will help to optimize the immunological properties of SAPNs.
Looking back at a quarter-century of research at the Maurice E. Müller Institute for Structural Biology.
Venue: Journal of structural biology

The Maurice E. Müller Institute, embedded in the infrastructure of the Biozentrum, University of Basel, was founded in 1985 and financed by the Maurice E. Müller Foundation of Switzerland. For 26 years its two founders, Ueli Aebi and Andreas Engel, pursued the vision of integrated structural biology. This paper reviews selected publications issuing from the Maurice E. Müller Institute for Structural Biology and marks the end of this era.