nils-herrmann/clean_scirepeval huggingface dataset:
A method for the quantification of the pressure dependent 3D collagen configuration in the arterial adventitia.
Venue: Journal of structural biology

Collagen plays an important role in the response of the arterial wall to mechanical loading and presumably has a load-bearing function preventing overdistension. Collagen configuration is important for understanding this role, in particular in mathematical models of arterial wall mechanics. In this study a new method is presented to image and quantify this configuration. Collagen in the arterial adventitia is stained with CNA35, and imaged in situ at high resolution with confocal microscopy at luminal pressures from 0 to 140mm Hg. The images are processed with a new automatic approach, utilizing techniques intended for MRI-DTI data. Collagen configuration is quantified through three parameters: the waviness, the transmural angle and the helical angle. The method is demonstrated for the case of carotid arteries of the white New Zealand rabbit. The waviness indicated a gradual straightening between 40 and 80mm Hg. The transmural angle was about zero indicating that the fibers stayed within an axial-circumferential plane at all pressures. The helical angle was characterized by a symmetrical distribution around the axial direction, indicating a double symmetrical helix. The method is the first to combine high resolution imaging with a new automatic image processing approach to quantify the 3D configuration of collagen in the adventitia as a function of pressure.
Nano-hierarchical structure and electromechanical coupling properties of clamshell.
Venue: Journal of structural biology

Electromechanical coupling is a nearly universal property of biomaterials, and may play an important role in many physiological and functional phenomena. The intrinsic or externally-generated electric field within biomaterials may also contribute to their predominant mechanical properties. Mollusc shells are well known for their outstanding mechanical properties, which are generally believed to originate from their hierarchical structures in multi-levels. This paper is therefore focused on the studies of the hierarchical structures and electromechanical coupling behaviors of clamshell from micro- to nano-levels, and in particular, the biopolymer concentrated regions. Detailed studies are performed to characterize the piezoelectric and ferroelectric properties of clamshell. It was found that the piezoresponse of clamshell is originated from the biopolymers between the mineral grains, as well as those intercalated within the mineral crystalline structure after the biomineralization process. Local ferroelectric hysteresis loops of clamshell have also been observed and analyzed on the samples with different orientations, biopolymer contents, or moisture contents. It is believed that the overall functioning of the clamshell or even other mollusc shells may incorporate many mechanisms interacting together, rather than originate from the hierarchical structure alone. This study of the electromechanical coupling effects of clamshell can be a path to have more comprehensive understandings of the properties and behaviors of mollusc shells.
Rescue of growth defects of yeast cdc48 mutants by pathogenic IBMPFD-VCPs.
Venue: Journal of structural biology

VCP/p97/Cdc48 is a hexameric ring-shaped AAA ATPase that participates in a wide variety of cellular functions. VCP is a very abundant protein in essentially all types of cells and is highly conserved among eukaryotes. To date, 19 different single amino acid-substitutions in VCP have been reported to cause IBMPFD (inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia), an autosomal dominant inherited human disease. Moreover, several similar single amino acid substitutions have been proposed to associate with a rare subclass of familial ALS. The mechanisms by which these mutations contribute to the pathogenesis are unclear. To elucidate potential functional differences between wild-type and pathogenic VCPs, we expressed both VCPs in yeast cdc48 mutants. We observed that all tested pathogenic VCPs suppressed the temperature-sensitive phenotype of cdc48 mutants more efficiently than wild-type VCP. In addition, pathogenic VCPs, but not wild-type VCP, were able to rescue a lethal cdc48 disruption. In yeast, pathogenic VCPs, but not wild-type VCP, formed apparent cytoplasmic foci, and these foci were transported to budding sites by the Myo2/actin-mediated transport machinery. The foci formation of pathogenic VCPs appeared to be associated with their suppression of the temperature-sensitive phenotype of cdc48 mutants. These results support the idea that the pathogenic VCP mutations create dominant gain-of-functions rather than a simple loss of functional VCP. Their unique properties in yeast could provide a convenient drug-screening system for the treatment of these diseases.
ATP-dependent assembly of the heteromeric Pex1p-Pex6p-complex of the peroxisomal matrix protein import machinery.
Venue: Journal of structural biology

The peroxisomal matrix protein import is facilitated by soluble receptor molecules which cycle between cytosol and the peroxisomal membrane. At the end of the receptor cycle, the import receptors are exported back to the cytosol in an ATP-dependent manner catalyzed by Pex1p and Pex6p, two AAA (ATPases associated with various cellular activities) type ATPases. Pex1p and Pex6p interact and form a heteromeric complex. In order to gain more insight into the stoichiometry and mechanism of assembly of the complex, we heterologously expressed and purified Saccharomyces cerevisiae Pex1p and Pex6p. Size exclusion chromatography studies of the recombinant proteins demonstrate that they form a hexameric complex in a one-to-one ratio of both AAA-proteins. The recombinant AAA-complex exhibits an ATPase activity with a k(m) of 0.17 mM and V(max) of 0.35 nmol min(-1) μg(-1). In the presence of N-ethylmaleimide, ATPase activity of the peroxisomal AAA-complex is drastically decreased and the complex dissociates. Disassembly of the complex into its Pex1p and Pex6p subunits is also observed upon ATP-depletion, indicating that formation of the Pex1p/Pex6p-complex requires the presence of ATP.
Substrate recognition and processing by a Walker B mutant of the human mitochondrial AAA+ protein CLPX.
Venue: Journal of structural biology

The mitochondrial matrix of mammalian cells contains several different ATP-dependent proteases, including CLPXP, some of which contribute to protein maturation and quality control. Currently however, the substrates and the physiological roles of mitochondrial CLPXP in humans, has remained elusive. Similarly, the mechanism by which these ATP-dependent proteases recognize their substrates currently remains unclear. Here we report the characterization of a Walker B mutation in human CLPX, in which the highly conserved glutamate was replaced with alanine. This mutant protein exhibits improved interaction with the model unfolded substrate casein and several putative physiological substrates in vitro. Although this mutant lacks ATPase activity, it retains the ability to mediate casein degradation by hCLPP, in a fashion similar to the small molecule ClpP-activator, ADEP. Our functional dissection of hCLPX structure, also identified that most model substrates are recognized by the N-terminal domain, although some substrates bypass this step and dock, directly to the pore-1 motif. Collectively these data reveal, that despite the difference between bacterial and human CLPXP complexes, human CLPXP exhibits a similar mode of substrate recognition and is deregulated by ADEPs.
Unique water distribution of Langmuir-Blodgett versus classical crystals.
Venue: Journal of structural biology

Langmuir-Blodgett films when used as nanotemplates for crystallization often leads to marked changes in protein stability and structure. Earlier we found that stability of proteins is also correlated with aqueous surroundings in the crystals. Here we study the direct relationships between presence of LB nanotemplates and unique patterns of water molecules surrounding the protein, for four model proteins for which 3D structures are available, and where crystallization conditions for each protein are the same except the presence of LB nanotemplate. Shape of frequency distribution of volumes occupied by water molecules were analyzed. They were found to be different between "classical" samples of different proteins, but surprisingly quite similar for LB samples. Volumes occupied by each water molecule as the function of the distance of the given molecule from the protein surface were studied. Introduction of LB film leads to appearance of water molecules close to protein surface but occupying large volumes. These findings confirm earlier experimental findings on the role of water molecules in determining protein stability and thereby pointing to water as a possible candidate for differences apparent in LB crystal stability against radiation.
The role of disulfide bond formation in the structural transition observed in the intermediate filaments of developing hair.
Venue: Journal of structural biology

Hair keratin is a composite structure in which intermediate filaments (IF) are embedded in a protein matrix. During the early stages of development in the hair follicle the redox potential is such that the cysteine residues in the IF are maintained in a reduced form. However, at a late stage of development the redox potential changes to produce an oxidizing environment and the IF undergo a structural transition involving both molecular slippage and radial compaction. In our earlier study the changes in the molecular parameters were estimated from knowledge of the sites of artificially induced crosslinks, and it was noted that the changes in these parameters realigned many of the cysteine residues to positions more favorable to disulfide bond formation. As the energy involved in the formation of disulfide bonds is much greater than that of hydrogen bonds or van der Waals interactions the structural transition is likely to be dominated by the requirement that the bonded cysteine residues occur at closely equivalent axial positions. This criterion was used in the present study to obtain more precise values for the molecular parameters in the oxidized fiber than has hitherto been possible. A comparison of the sequences of hair keratins and epidermal keratins suggests that the slippage observed in trichocyte IF during keratinization does not occur in epidermal IF.
Visualization of sub-daily skeletal growth patterns in massive Porites corals grown in Sr-enriched seawater.
Venue: Journal of structural biology

We performed high resolution marking experiments using seawater with elevated Sr concentration to investigate the timing and ultrastructure of skeletal deposition by massive Porites australiensis corals. Corals were cultured in seawater enriched with Sr during day-time only, night-time only or for one full-day. Cross sections of skeletal material were prepared and the Sr incorporated into the newly deposited skeleton analyzed by electron probe microanalysis. These regions of Sr incorporation were then correlated with skeletal ultrastructure. Massive Porites coral skeletons are composed of two types of microstructural elements - the "centers of calcification" and the surrounding fibrous structural region. Within the fibrous structural region, alternative patterns of etch-sensitive growth lines and an etch-resistant fibrous layer were observed. In the full-day samples, high-Sr bands extended across both growth lines and fibrous layers. In day-time samples, high-Sr regions corresponded to the fibrous layer, while in the night-time samples high-Sr regions were associated with an outermost growth line. These distinct growth patterns suggest a daily growth pattern associated with the fibrous region of massive P. australiensis corals, where a pair of narrow growth lines and a larger fibrous layer is seen as a daily growth region.
Improving the quality of electron tomography image volumes using pre-reconstruction filtering.
Venue: Journal of structural biology

Electron tomography produces highly magnified 3D image volumes useful for investigating the structure and function of cellular components. Image quality is degraded by multiple scattering events and quantum noise, which depend on the angle at which individual tilt projections are collected. We have adapted a biomedical imaging approach to improve image quality by enhancing individual tilt projections prior to volumetric reconstruction. Specifically, we have developed a family of non-linear anisotropic diffusion (NAD) filters parameterized by the tilt angle. We give a quantitative and qualitative evaluation of our pre-processing approach and the NAD filter. We show an improvement in the reconstructed volumes for tomograms generated from both plastic-embedded and cryo-stabilized samples of malaria parasite-infected erythrocytes.
The influence of ATP-dependent proteases on a variety of nucleoid-associated processes.
Venue: Journal of structural biology

ATP-dependent proteases are crucial components of all living cells and are involved in a variety of responses to physiological and environmental changes. Nucleoids are dynamic nucleoprotein complexes present in bacteria and eukaryotic organelles (mitochondria and plastids) and are the place where the majority of cellular responses to stress begin. These structures are actively remodeled in reaction to changing environmental and physiological conditions. The levels of nucleoid protein components (e.g. DNA-stabilizing proteins, transcription factors, replication proteins) therefore have to be continually regulated. ATP-dependent proteases have all the characteristics needed to fulfill this requirement. Some of them bind nucleic acids, but above all, they control and maintain the level of many DNA-binding proteins. In this review we will discuss the roles of the Lon, ClpAP, ClpXP, HslUV and FtsH proteases in the maintenance, stability, transcription and repair of DNA in eubacterial and mitochondrial nucleoids.
Structural biology of cytoplasmic and axonemal dyneins.
Venue: Journal of structural biology

Dyneins are microtubule-based, ATP-driven motor proteins with six tandemly linked AAA+ domains, a long N-terminal tail and a coiled-coil stalk. Cytoplasmic dyneins function as individual homodimers and are responsible for minus-end-oriented transport along microtubules. Axonemal dyneins of flagella/cilia are anchored in arrays to peripheral microtubule doublets by their N-terminal tails, and generate sliding motions of adjacent microtubule doublets toward the plus end. The coiled-coil stalk is responsible for communication between the AAA+ domains and the microtubule binding domain. A number of isoforms of axonemal dyneins are integrated to generate bending motion. In this article I will review recent structural studies and address the question as to how dyneins generate force and cause bending in flagella/cilia.
Mapping the road to recovery: the ClpB/Hsp104 molecular chaperone.
Venue: Journal of structural biology

The AAA(+)-ATPases are a family of molecular motors which have been seconded into a plethora of cellular tasks. One subset, the Hsp100 molecular chaperones, are general protein remodellers that help to maintain the integrity of the cellular proteome by means of protein destruction or resurrection. In this review we focus on one family of Hsp100s, the homologous ClpB and Hsp104 molecular chaperones that convey thermotolerance by resolubilising and rescuing proteins from aggregates. We explore how the nucleotide binding and hydrolysis properties at the twelve nucleotide-binding domains of these hexameric rings are coupled to protein disaggregation, highlighting similarities and differences between ClpB and Hsp104.
Determining pair distance distribution function from SAXS data using parametric functionals.
Venue: Journal of structural biology

Small angle X-ray scattering (SAXS) experiments are widely applied in structural biology. The SAXS experiments yield one-dimensional profile that needs further analysis to reveal structural information. The pair distance distribution function (PDDF), P(r), can provide molecular structures more intuitively, and it can be used to guide ab initio model reconstructions, making it a critical step to derive P(r) from experimental SAXS profiles. To calculate the P(r) curves, a new method based on a specially designed parametric functional form is developed, and implemented in pregxs. This method is tested against both synthetic and experimental data, the estimated P(r) functions are in good agreement with correct or known P(r). The method can also predict the molecular size. In summary, the pregxs method is robust and accurate in P(r) determination from SAXS profiles. The pregxs source code and an online server are available at http://www.sastbx.als.lbl.gov.
Calcium bodies of Titanethes albus (Crustacea: Isopoda): molt-related structural dynamics and calcified matrix-associated bacteria.
Venue: Journal of structural biology

Crustaceans form a variety of calcium deposits in which they store calcium necessary for the mineralization of their exoskeletons. Calcium bodies, organs containing large amounts of calcium, have been reported in some terrestrial isopod crustaceans, but have not yet been extensively studied. We analyzed the architecture of these organs during the molt cycle in the isopod Titanethes albus. Two pairs of calcium bodies are positioned ventrolaterally in posterior pereonites of T. albus. Individual organs are epithelial sacs that contain material arranged in concentric layers delimited by thin laminae. As demonstrated by electron microscopy and fluorescence in situ hybridization, abundant bacteria are present within the calcium bodies. Regardless of the molt cycle stage, crystalline concretions are present in the central areas of the calcium bodies. Energy dispersive X-ray spectrometry of the concretions demonstrated that they are composed predominantly of calcium and phosphorus and selected area electron diffraction indicated the presence of hydroxyapatite. In molting animals, a glassy layer of mineralized matrix is formed between the envelope and the outermost lamina of the calcium body. This layer consists of an amorphous calcium mineral which contains less phosphorus than the central concretions and is resorbed after molt. Since changes in the mineralized matrix are synchronized with the molt cycle, the calcium bodies likely function as a storage compartment that complements sternal deposits as a source of calcium for the mineralization of the exoskeleton. Bacteria associated with the mineralized matrix of calcium bodies are evidently involved in calcium dynamics.
High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.
Venue: Journal of structural biology

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.
Theoretical investigation of quinone metabolites of dopamine interaction with DNA--insights into toxicological effects.
Venue: Journal of structural biology

Dopamine (3,4-dihydroxyphenylethylamine, DA), an important neurotransmitter, exists in the cell bodies of the dopaminergic neurons of the substantia nigra. Oxidation of DA to its quinone and subsequent reaction with Adenine and Guanine in DNA result in the formation of depurinating adducts, thus causing DNA damage. In this article, we investigate the interaction of quinone metabolites of dopamine (DMQ) with models representing the structure of DNA using dispersion corrected density functional theory with an aim to evaluate the associated structural changes in DNA upon their interaction. Various binding sites for the DA metabolite on these DNA models have been considered and our computations on the activation barriers allowed us to identify preferential bonding sites for these metabolites analogous to experiments. Analysis of the geometry of these adducts in comparison to free base pairs reveals that the attack of DMQ causes remarkable changes in the structural properties. With our calculations, we propose that these structural alterations induce mutations by favoring the formation of depurinating adducts leading to mutagenic effects such as base mispairing, explaining the toxicological (carcinogenic and neurotoxic) behavior of DMQ.
Functional analysis of conserved cis- and trans-elements in the Hsp104 protein disaggregating machine.
Venue: Journal of structural biology

Hsp104 is a double ring-forming AAA+ ATPase, which harnesses the energy of ATP binding and hydrolysis to rescue proteins from a previously aggregated state. Like other AAA+ machines, Hsp104 features conserved cis- and trans-acting elements, which are hallmarks of AAA+ members and are essential to Hsp104 function. Despite these similarities, it was recently proposed that Hsp104 is an atypical AAA+ ATPase, which markedly differs in 3D structure from other AAA+ machines. Consequently, it was proposed that arginines found in the non-conserved M-domain, but not the predicted Arg-fingers, serve the role of the critical trans-acting element in Hsp104. While the structural discrepancy has been resolved, the role of the Arg-finger residues in Hsp104 remains controversial. Here, we exploited the ability of Hsp104 variants featuring mutations in one ring to retain ATPase and chaperone activities, to elucidate the functional role of the predicted Arg-finger residues. We found that the evolutionarily conserved Arg-fingers are absolutely essential for ATP hydrolysis but are dispensable for hexamer assembly in Hsp104. On the other hand, M-domain arginines are not strictly required for ATP hydrolysis and affect the ATPase and chaperone activities in a complex manner. Our results confirm that Hsp104 is not an atypical AAA+ ATPase, and uses conserved structural elements common to diverse AAA+ machines to drive the mechanical unfolding of aggregated proteins.