nils-herrmann/clean_scirepeval huggingface dataset:
A Biophysical and Structural Analysis of the Interaction of BLNK with 14-3-3 Proteins.
Venue: Journal of structural biology

B-cell linker protein (BLNK) is an adaptor protein that orchestrates signalling downstream of B-cell receptors. It has been reported to undergo proteasomal degradation upon binding to 14-3-3 proteins. Here, we report the first biophysical and structural study of this protein-protein interaction (PPI). Specifically, we investigated the binding of mono- and di- phosphorylated BLNK peptides to 14-3-3 using fluorescent polarization (FP) and isothermal titration calorimetry assays (ITC). Our results suggest that BLNK interacts with 14-3-3 according to the gatekeeper model, where HPK1 mediated phosphorylation of Thr152 (pT152) allows BLNK anchoring to 14-3-3, and an additional phosphorylation of Ser285 (pS285) by AKT, then further improves the affinity. Finally, we have also solved a crystal structure of the BLNKpT152 peptide bound to 14-3-3σ. These findings could serve as important tool for compound discovery programs aiming to modulate this interaction with 14-3-3.
Structural basis for inhibitory effects of Smad7 on TGF-β family signaling.
Venue: Journal of structural biology

Smad6 and Smad7 are classified as inhibitory Smads (I-Smads). They are crucial in the fine-tuning of signals by cytokines of the transforming growth factor-beta (TGF-β) family. They are negative feedback regulators and principally target the activated type I receptors as well as the activated Smad complexes, but with distinct specificities. Smad7 inhibits Smad signaling from all seven type I receptors of the TGF-β family, whereas Smad6 preferentially inhibits Smad signaling from the bone morphogenetic protein (BMP) type I receptors, BMPR1A and BMPR1B. The target specificities are attributed to the C-terminal MH2 domain. Notably, Smad7 utilizes two alternative molecular surfaces for its inhibitory function against type I receptors. One is a basic groove composed of the first α-helix and the L3 loop, a structure that is shared with Smad6 and receptor-regulated Smads (R-Smads). The other is a three-finger-like structure (consisting of residues 331-361, 379-387, and the L3 loop) that is unique to Smad7. The underlying structural basis remains to be elucidated in detail. Here, we report the crystal structure of the MH2 domain of mouse Smad7 at 1.9 Å resolution. The three-finger-like structure is stabilized by a network of hydrogen bonds between residues 331-361 and 379-387, thus forming a molecular surface unique to Smad7. Furthermore, we discuss how Smad7 antagonizes the activated Smad complexes composed of R-Smad and Smad4, a common partner Smad.
Structural basis for promoter DNA recognition by the response regulator OmpR.
Venue: Journal of structural biology

OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR-DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc-DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this "druggable" target.
Investigation of the human pineal gland 3D organization by X-ray phase contrast tomography.
Venue: Journal of structural biology

Pineal gland (PG) is a part of the human brain epithalamus that plays an important role in sleep, circadian rhythm, immunity, and reproduction. The calcium deposits and lesions in PG interfere with normal function of the organ and can be associated with different health disorders including serious neurological diseases. At the moment, the detailed mechanisms of PG calcifications and PG lesions formation as well as their involvement in pathological processes are not fully understood. The deep and comprehensive study of the structure of the uncut human PG with histological details, poses a stiff challenge to most imaging techniques, due to low spatial resolution, low visibility or to exceedingly aggressive sample preparation. Here, we investigate the whole uncut and unstained human post-mortem PGs by x-ray phase contrast tomography (XPCT). XPCT is an advanced 3D imaging technique, that permits to study of both soft and calcified tissue of a sample at different scales: from the whole organ to cell structure. In our research we simultaneously resolved 3D structure of parenchyma, vascular network and calcifications. Moreover, we distinguished structural details of intact and degenerated PG tissue. We discriminated calcifications with different structure, pinealocytes nuclei and the glial cells processes. All results were validated by histology. Our research clear demonstrated that XPCT is a potential tool for the high resolution 3D imaging of PG morphological features. This technique opens a new perspective to investigate PG dysfunction and understand the mechanisms of onset and progression of diseases involving the pineal gland.
Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme.
Venue: Journal of structural biology

The removal of carbon dioxide from the waste streams of industrial processes is a major challenge for creation of a sustainable circular economy. This makes the synthesis of formate from CO2 by NAD+ dependent formate dehydrogenases (FDHs) an attractive process for this purpose. The efficiency of this reaction is however low and to achieve a viable industrial process an optimised engineered enzyme needs to be developed. In order to understand the detailed enzymatic mechanism of catalysis structures of different cofactor and substrate complexes of the FDH from the thermophilic filamentous fungus, Chaetomium thermophilum have been determined to 1.2-1.3 Å resolution. The substrate formate is shown to be held by four hydrogen bonds in the FDH catalytic site within the ternary complex with substrate and NAD+and a secondary formate binding site is observed in crystals soaked with substrate. Water molecules are excluded from the FDH catalytic site when the substrate is bound. The angle between the plane of the NAD+ cofactor pyridine ring and the plane of the formate molecule is around 27°. Additionally, structures of a FDH mutant enzyme, N120C, in complex with the reduced form of the cofactor have also been determined both in the presence and absence of formate bound at the secondary site. These structures provide further understanding of the catalytic mechanism of this fungal enzyme.
Orientation patterns of aragonitic crossed-lamellar, fibrous prismatic and myostracal microstructures of modern Glycymeris shells.
Venue: Journal of structural biology

The shells of the bivalves Glycymeris glycymeris and Glycymeris nummaria are widely used for environmental studies. They consist of aragonite and comprise four different microstructures and textures from outer to inner shell surfaces: crossed-lamellar, myostracal, complex crossed-lamellar and fibrous prismatic. We characterize with SEM, EBSD, laser-confocal microscopy and AFM imaging mineral unit size, morphology and orientation of crystallites in the different microstructural arrangements and at the transition from one microstructure to the other. We also characterize the microstructure and texture of adductor and pedal retractor myostraca and address structural characteristics at the transition from crossed-lamellar to myostracal assemblies. We find that the crossed-lamellar layer has a three-dimensional crystallographic orientational order. Each set of first-order lamellae consists of twinned aragonite; the two sets of first-order lamellae are misoriented to each other by about 30 to 40° while retaining an approximately parallel a-axis; they do not show any particular twin relationship. Myostracal aragonite grows homoepitactically onto the crossed-lamellar aragonite, but is clearly a separate microstructure, with its own crystallite size and morphology. Within adductor and pedal myostraca, prisms increase in size towards inner surfaces. In contrast to the other shell layers, the myostraca form through competitive growth. The complex crossed-lamellar aragonite initially inherits the three-dimensional texture of the crossed-lamellar microstructure, but with growth develops an axial texture, which is transmitted to the underlying fibrous prismatic microstructure. With this work we provide a modern, unaltered, reference for fossil Glycymeris shells to be used for detection of diagenetic overprint in fossil Glycymeris analogs.
Insight into human Miro1/2 domain organization based on the structure of its N-terminal GTPase.
Venue: Journal of structural biology

Dysfunction in mitochondrial dynamics is believed to contribute to a host of neurological disorders and has recently been implicated in cancer metastasis. The outer mitochondrial membrane adapter protein Miro functions in the regulation of mitochondrial mobility and degradation, however, the structural basis for its roles in mitochondrial regulation remain unknown. Here, we report a 1.7Å crystal structure of N-terminal GTPase domain (nGTPase) of human Miro1 bound unexpectedly to GTP, thereby revealing a non-catalytic configuration of the putative GTPase active site. We identify two conserved surfaces of the nGTPase, the "SELFYY" and "ITIP" motifs, that are potentially positioned to mediate dimerization or interaction with binding partners. Additionally, we report small angle X-ray scattering (SAXS) data obtained from the intact soluble HsMiro1 and its paralog HsMiro2. Taken together, the data allow modeling of a crescent-shaped assembly of the soluble domain of HsMiro1/2. PDB RSEFERENCE: Crystal structure of the human Miro1 N-terminal GTPase bound to GTP, 6D71.
Cryo-EM analysis of the SctV cytosolic domain from the Enteropathogenic E.coli T3SS injectisome.
Venue: Journal of structural biology

The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, through which signal-modulating effector proteins are secreted. The inner membrane pore protein SctV controls the hierarchy of substrate selection and may also be involved in energizing secretion. We present the 4.7 Å cryo-EM structure of the SctV cytosolic domain (SctVC) from the enteropathogenic Escherichia coli injectisome. SctVC forms a nonameric ring with primarily electrostatic interactions between its subunits. Molecular dynamics simulations show that monomeric SctVC maintains a closed conformation, in contrast with previous studies on flagellar homologue FlhA. Comparison with substrate-bound homologues suggest that a conformational change would be required to accommodate binding partners.
A computer-simulated mechanism of familial Alzheimer's disease: Mutations enhance thermal dynamics and favor looser substrate-binding to γ-secretase.
Venue: Journal of structural biology

The 4-subunit intramembrane protease complex γ-secretase cleaves many substrates including fragments of the β-amyloid precursor protein (APP), leading to formation of Aβ peptides, and Notch. Mutations in APP and the catalytic subunit of γ-secretase, presenilin, cause familial Alzheimer's disease (fAD). Mutations are assumed to change the substrate-binding and cleavage and thereby the Aβ formed. Whereas a wild-type structure of substrate-bound γ-secretase became recently available from cryogenic electron microscopy (6IYC), the structure and dynamics of mutant proteins remain obscure. Here, we studied five prominent mutants of substrate-bound γ-secretase by explicit all-atom molecular dynamics in a phospholipid membrane model at physiological temperature using the experimental structure as template: The presenilin 1 mutants E280A, G384A, A434C, and L435F and the V717I mutant of APP. Our structures and dynamics provide the first atomic detail into how fAD-causing mutations affect substrate binding to γ-secretase. The pathogenic mutations tend to increase the space and variability in the substrate binding site, as seen e.g. from the distance from catalytic aspartate to substrate cleavage sites. We suggest that we have identified the molecular cause of the "imprecise cleavage" that leads to two trimming pathways in γ-secretase, consistent with the FIST model, which may rationalize the experimental Aβ42/Aβ40 ratios as a molecular basis for fAD.
External bone size identifies different strength-decline trajectories for the male human femora.
Venue: Journal of structural biology

Understanding skeletal aging and predicting fracture risk is increasingly important with a growing elderly population. We hypothesized that when categorized by external bone size, the male femoral diaphysis would show different strength-age trajectories which can be explained by changes in morphology, composition and collagen cross-linking. Cadaveric male femora were sorted into narrow (n = 15, 26-89 years) and wide (n = 15, 29-82 years) groups based upon total cross-sectional area of the mid-shaft normalized to bone length (Tt.Ar/Le) and tested for whole bone strength, tissue-level strength, and tissue-level post-yield strain. Morphology, cortical TMD (Ct.TMD), porosity, direct measurements of enzymatic collagen cross-links, and pentosidine were obtained. The wide group alone showed significant negative correlations with age for tissue-level strength (R2 = 0.50, p = 0.002), tissue-level post-yield strain (R2 = 0.75, p < 0.001) and borderline significance for whole bone strength (R2 = 0.14, p = 0.108). Ct.TMD correlated with whole bone and tissue-level strength for both groups, but pentosidine normalized to enzymatic cross-links correlated negatively with all mechanical properties for the wide group only. The multivariate analysis showed that just three traits for each mechanical property explained the majority of the variance for whole bone strength (Ct.Area, Ct.TMD, Log(PEN/Mature; R2 = 0.75), tissue-level strength (Age, Ct.TMD, Log(DHLNL/HLNL); R2 = 0.56), and post-yield strain (Age, Log(Pyrrole), Ct.Area; R2 = 0.51). Overall, this highlights how inter-individual differences in bone structure, composition, and strength change with aging and that a one-size fits all understanding of skeletal aging is insufficient.
Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8.
Venue: Journal of structural biology

Recent reports indicate the Type six secretion system exported effector 8 (Tse8) is a cytoactive effector secreted by the Type VI secretion system (T6SS) of the human pathogen Pseudomonas aeruginosa. The T6SS is a nanomachine that assembles inside of the bacteria and injects effectors/toxins into target cells, providing a fitness advantage over competing bacteria and facilitating host colonisation. Here we present the first crystal structure of Tse8, showing it conserves a putative catalytic triad Lys84-transSer162-Ser186 found among homologues. Furthermore, we measure the binding of phenylmethylsulfonyl fluoride (PMSF) to Tse8. Remarkably, we observed that PMSF binding is dependent on the putative catalytic residue Ser186, providing evidences of its nucleophilic reactivity. This work demonstrates that Tse8 belongs to the Amidase Signature (AS) superfamily. Furthermore, it highlights Tse8 similarity to two family members: the Stenotrophomonas maltophilia Peptide Amidase, and the Glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus.
Crystal structure and enzymatic characterization of the putative adenylyl cyclase HpAC1 from Hippeastrum reveal dominant triphosphatase activity.
Venue: Journal of structural biology

HpAC1, a protein from Hippeastrum hybrid cultivars, was previously suggested to be a plant adenylyl cyclase. We describe a structural and enzymatic characterization of HpAC1. A crystal structure of HpAC1 in complex with a non-hydrolyzable GTP analog confirms a generic CYTH architecture, comprising a b-barrel with an internal substrate site. The structure reveals significant active site differences to AC proteins with CYTH fold, however, and we find that HpAC1 lacks measurable AC activity. Instead, HpAC1 has substantial triphosphatase activity, indicating this protective activity or a related activity as the protein's physiological function.
Unit quaternion description of spatial rotations in 3D electron cryo-microscopy.
Venue: Journal of structural biology

Electron cryo-microscopy (cryoEM) involves the estimation of spatial rotations, or saying orientations, of projection images or three-dimensional (3D) volumes. Euler angle system is widely used to describe spatial rotations in most cryoEM algorithms and software. In this review, we introduce unit quaternion as an alternate to Euler angles for describing spatial rotations, customize and develop corresponding tools for increasing demands of statistical analysis of spatial rotations in cryoEM. Some basic properties and definitions of quaternion are first recalled. Thereafter, distance and geodesic between rotations are introduced to aid comparisons and interpolations between rotations, which are prerequisites of statistics of rotations in 3D cryoEM. Furthermore, statistics of rotations are reviewed. Techniques potentially useful in cryoEM, such as calculations of the average rotation, generation of quasi-regular grids, sampling, inference with uniform distribution and angular central Gaussian (ACG) distribution, and estimation of rotation precision, are reviewed and developed. Finally, molecular symmetry presented in unit quaternion form is discussed. Unit quaternion system is shown as a convenient and comprehensive mathematical tool for cryoEM.
Elastin calcification in in vitro models and its prevention by MGP's m3pS peptide.
Venue: Journal of structural biology

Medial calcification has been associated with diabetes, chronic kidney disease, and genetic disorders like pseudoxanthoma elasticum. Recently, we showed that genetic reduction of arterial elastin content reduces the severity of medial calcification in matrix Gla protein (MGP)-deficient and Eln haploinsufficient Mgp-/-;Eln+/- mice. This study suggests that there might be a direct effect of elastin amount on medial calcification. We studied this in vitro, using novel in vitro systems, which are based on elastin or elastin-like polypeptides. We first examined the mineral deposition properties of a transfected pigmented epithelial cell line that expresses elastin and other elastic lamina proteins. When grown in inorganic phosphate-supplemented medium, these cells deposited calcium phosphate minerals, which could be prevented by an N'-terminal peptide of MGP (m3pS) carrying phosphorylated serine residues. We next confirmed these findings using a cell-free elastin-like polypeptide (ELP3) scaffold, where the peptide prevented mineral maturation. Overall, this work describes a novel cell culture model for elastocalcinosis and examines the inhibition of mineral deposition by the m3pS peptide in this and a cell-free elastin-based scaffold. Our study provides strong evidence suggesting the critical functional roles of MGP's phosphorylated serine residues and proposes a possible mechanism of their action.
Characterization and Functional Insights into the Entamoeba histolytica Pyridoxal Kinase, an Enzyme Essential for its Survival.
Venue: Journal of structural biology

Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B6 and a cofactor for more than 140 enzymes. This coenzyme plays a pivotal role in catalysis of various enzymatic reactions that are critical for the survival of organisms. Entamoeba histolytica depends on the uptake of pyridoxal (PL), a B6 vitamer from the external environment which is then phosphorylated by pyridoxal kinase (EhPLK) to form PLP via the salvage pathway. E. histolytica cannot synthesise vitamin B6de-novo, and also lacks pyridoxine 5'-phosphate oxidase, a salvage pathway enzyme required to produce PLP from pyridoxine phosphate (PNP) and pyridoxamine phosphate (PMP). Analysing the importance of PLK in E. histolytica, we have determined the high-resolution crystal structures of the dimeric pyridoxal kinase in apo, ADP-bound, and PLP-bound states. These structures provided a snapshot of the transition state and help in understanding the reaction mechanism in greater detail. The EhPLK structure significantly differed from the human homologue at its PLP binding site, and the phylogenetic study also revealed its divergence from human PLK. Further, gene regulation of EhPLK using sense and antisense RNA showed that any change in optimal level is harmful to the pathogen. Biochemical and in vivo studies unveiled EhPLK to be essential for this pathogen, while the molecular differences with human PLK structure can be exploited for the structure-guided design of EhPLK inhibitors.
Embedding cells within nanoscale rapidly mineralizing hydrogels: a new paradigm to engineer cell-laden bone-like tissue.
Venue: Journal of structural biology

Bone mineralization is a highly specific and dynamic nanoscale process that has been studied extensively from a structural, chemical, and biological standpoint. Bone tissue, therefore, may be defined by the interplay of its intricately mineralized matrix and the cells that regulate its biological function. However, the far majority of engineered bone model systems and bone replacement materials have been unable to replicate this key characteristic of bone tissue; that is, the ability of cells to be gradually and rapidly embedded in a three-dimensional (3D) heavily calcified matrix material. Here we review the characteristics that define the bone matrix from a nanostructural perspective. We then revisit the benefits and challenges of existing model systems and engineered bone replacement materials, and discuss recent efforts to replicate the biological, cellular, mechanical, and materials characteristics of bone tissue on the nano- to microscale. We pay particular attention to a recently proposed method developed by our group, which seeks to replicate key aspects of the entrapment of bone cells within a mineralized matrix with precisions down to the level of individual nano-crystallites, inclusive of the bone vasculature, and osteogenic differentiation process. In summary, this paper discusses existing and emerging evidence pointing towards future developments bridging the gap between the fields of biomineralization, structural biology, stem cells, and tissue engineering, which we believe will hold the key to engineer truly functional bone-like tissue in the laboratory.