Double Domain Research Articles

Cone snail prolyl-4-hydroxylase α-subunit sequences derived from transcriptomic data and mass spectrometric analysis of variable proline hydroxylation in C. amadis venom

Putative prolyl-4-hydroxylase (P4H) α-subunit sequences have been extracted by mining transcriptomic data obtained from seven cone snail species C. amadis, C. monile, C. araneosus, C. miles, C. litteratus, C. frigidus, and C. ebraeus. Sequences ranging from 518 to 559 residues have been compared with representative animal P4H sequences. The α-subunit consists of an N-terminus double domain, involved in dimerization and substrate binding, while the C-terminus contains the catalytic domain. Definitive functional annotation of the cone snail sequences has been achieved by an analysis of conserved residues responsible for catalytic function, specific conformational features, and subunit interactions, using two independent structures of the double domain, and the catalytic domain, previously reported in the literature. The variability of proline hydroxylation in conotoxins is illustrated by a mass spectrometric analysis of C. amadis venom. Site specific hydroxylation and the presence of peptides with multiple proline residues, resistant to modification, suggests that sequence and conformational effects may determine the substrate specificity of the Conus prolyl-4-hydroxylases. SignificanceProline hydroxylation is a widely observed post translational modification, with collagen being the pre-eminent example. Hydroxylation of proline is also widely observed in conotoxins, which are a major component of marine cone snail venom. This paper describes newly identified prolyl-4-hydroxylase sequences, using transcriptome data from seven Conus species. The predicted functional annotation of prolyl-4-hydroxylase sequences was carried out using two available crystal structures of independent domains. The mass spectrometric characterisation of proline/hydroxyproline containing peptides in C. amadis venom confirms sequence specific hydroxylation in Conus venom as shown previously by others.

Vacuum Constraints for Realistic Strongly Coupled Heterotic M-Theories

The compactification from the 11-dimensional Horava-Witten orbifold to 5-dimensional heterotic M-theory on a Schoen Calabi-Yau threefold is reviewed, as is the specific S U ( 4 ) vector bundle leading to the “heterotic standard model” in the observable sector. A generic formalism for a consistent hidden sector gauge bundle, within the context of strongly coupled heterotic M-theory, is presented. Anomaly cancellation and the associated bulk space 5-branes are discussed in this context. The further compactification to a 4-dimensional effective field theory on a linearized BPS double domain wall is then presented to order κ 11 4 / 3 . Specifically, the generic constraints required for anomaly cancellation and by the linearized domain wall solution, restrictions imposed by the vanishing of the D-terms and, finally, the constraints imposed by the necessity for positive, perturbative squared gauge couplings to this order are presented in detail.

Negative-temperature-state relaxation and reservoir-assisted quantum entanglement in double-spin-domain systems

Spin collective phenomena including superradiance are even today being intensively investigated with experimental tests performed based on state-of-the-art quantum technologies. Such attempts are not only for the simple experimental verification of predictions from the last century but also as a motivation to explore new applications of spin collective phenomena and the coherent control of the coupling between spin ensembles and reservoirs. In this paper, we investigate the open quantum dynamics of two spin ensembles (double spin domains) coupled to a common bosonic reservoir. We analyze in detail the dynamics of our collective state and its structure by focusing on both the symmetry and asymmetry of this coupled spin system. We find that when the spin size of one of the double domains is larger than that of the other domain, at the steady state this system exhibits two novel collective behaviors: the negative-temperature state relaxation in the smaller spin domain and the reservoir-assisted quantum entanglement between the two domains. These results are the consequence of the asymmetry of this system and the decoherence driven by the common reservoir.

Fusarium graminearum KP4-like proteins possess root growth-inhibiting activity against wheat and potentially contribute to fungal virulence in seedling rot

The virally encoded KP4 killer toxin protein was first identified from Ustilago maydis (Um), and its homologues are present in diverse fungi and in one species of moss. No KP4-like (KP4L) proteins have been functionally characterized. Here, we report the identification and functional analysis of four KP4L proteins from Fusarium graminearum (Fg), the primary causal pathogen of Fusarium head blight (FHB), which is also known to associate with seedling rot of wheat. The four FgKP4L proteins (FgKP4L-1, -2, -3 and -4) are encoded by small open reading frames (378–825 bp) located on chromosome 1 with the FgKP4L-1, -2 and -3 genes clustering together. Sequence analysis indicated that FgKP4L proteins have conserved domains predicted to form a three-dimensional alpha/beta-sandwich structure as first reported for UmKP4, with FgKP4L-4 featuring double Kp4 domains. Further analyses revealed that the FgKP4L genes are expressed in vitro under certain stress conditions, and all up-regulated during FHB and/or seedling rot development, the recombinant FgKP4L-2 protein does not induce cell death in wheat leaves or spikelets, but inhibits root growth of young seedlings, and the elimination of the FgKP4L-1/-2/-3 gene cluster from the fungal genome results in reduced virulence in seedling rot but not in FHB. Database searches revealed KP4L proteins from ∼80 fungal species with more than half from human/animal pathogens. Phylogenetic analysis suggested that UmKP4 and the moss KP4L proteins are closely related to those from a zygromycete and Aspergillus, respectively, implying cross-kingdom horizontal gene transfer.

Local valence electronic states of silicon (sub)oxides on HfO2/Si-(sub)oxide/Si(110) and HfSi2/Si-(sub)oxide/Si(110) Islands

The effect on the local valence electronic states of Sin+ suboxide components (n = 2, 3, and 4) of hafnium deposited on a low-index Si(110) substrate is investigated by Si-L23VV Auger electron Sin+-2p photoelectron coincidence spectroscopy (Si-L23VV-Sin+-2p APECS), and the chemical states and stabilities are discussed. Hafnium-covered Si(110) is immediately oxidized to HfO2 and SiO2 because hafnium serves as an effective catalyst for Si oxidation. Therefore, a HfO2/Sin+-(sub)oxide/Si(110) [HfO2/Sin+/Si(110)] structure is easily formed (n = 1, 2, 3, and 4). Oxygen diffusion from HfO2 layers toward the Si(110) substrate is promoted by annealing at 923 K. Oxygen atom desorption from the HfO2/Sin+/Si(110) surface occurs after annealing at 1073 K, and HfSi2 islands (i-HfSi2) are formed with a partly exposed Si(110)-16 × 2 double domain (DD) surface. i-HfSi2 shows low reactivity toward O2 molecules, whereas the exposed Si(110)-16 × 2 DD surface is immediately oxidized. Here, a i-HfSi2/Sin+-(sub)oxide/Si(110) (i-HfSi2/Sin+/Si(110)) structure is formed. Furthermore, we measure the Si-L23VV-Sin+-2p APECS spectra of Sin+ in the HfO2/Sin+/Si(110) and the i-HfSi2/Sin+/Si(110) structures (n = 2, 3, and 4) to evaluate the local valence electronic states of the Sin+ (sub)oxide components. The binding energy at the valence band maximum (BEVBM) of Sin+ in the i-HfSi2/Sin+/Si(110) structure is lower than 1.5 ± 0.7 eV as compared to that in the HfO2/Sin+/Si(110) structure (n = 2, 3, and 4). The local valence electric states of the nearest neighbors and the second neighbors through oxygen of Sin+ are determined to affect those of the Sin+ atom (n = 2, 3, and 4). The Sin+ atoms in the i-HfSi2/Sin+/Si(110) structure can directly bond to hafnium atoms as the nearest neighbors and most commonly have Sim+ atoms in lower ionic valence states as second neighbors (m < 4), whereas the Sin+ atoms in the HfO2/Sin+/Si(110) structure cannot form this bond. In addition, the existence of Hf silicide and Si in lower ionic valence states can reduce the band gap of the HfO2/Si(110) structure.

Sequence specific 1H, 13C and 15N resonance assignments of the C-terminal domain of human γS-crystallin.

The high solubility and stability of crystallins present in the human eye lens maintains its transparency and refractive index with negligible protein turnover. Monomeric γ-crystallins and oligomeric β-crystallins are made up of highly homologous double Greek key domains. These domains are symmetric and possess higher stability as a result of the complex topology of individual Greek key motifs. γS-crystallin is one of the most abundant structural βγ-crystallins present in the human eye lens. In order to understand the structural stability of individual domains of human γS-crystallin in isolation vis-à-vis full length protein, we set out to structurally characterize its C-terminal domain (abbreviated hereafter as γS-CTD) by solution NMR. In this direction, we have cloned, over-expressed, isolated and purified the γS-CTD. The 2D [15N-1H] HSQC recorded with uniformly 13C/15N labeled γS-CTD showed a highly dispersed spectrum indicating the protein to adopt an ordered conformation. In this paper, we report almost complete sequence-specific 1H, 13C and 15N resonance assignments of γS-CTD using a suite of heteronuclear 3D NMR experiments.

${\boldsymbol~K}$-fields domain wall

In this paper, we construct the single kink and double kink domain wall solutions by considering the non-canonical $K$-field in a flat five-dimensional spcaetime. The localization of chiral fermion is also investigated with the Yukawa coupling mechanism, and the corresponding massless left-chiral fermion can be localized on the $K$-field two types domain walls. The effective potentials of the chiral fermion on the two types domain walls will have different behaviors and the corresponding effective potential of the chiral fermion on the double-kink domain wall will have double well, and which means that the double kink domain wall will have mroe richer internal structures.

Platelet exocytosis protein DOC2B is an early biomarker of type 1 diabetes

Efforts to preserve β-cell mass in the preclinical stages of type 1 (T1D) are limited by few blood-derived biomarkers of β-cell destruction. Platelets are proposed to be the sources of blood-derived biomarkers for a variety of diseases, and they show distinct proteomic changes in T1D. Thus, studying these proteomic changes may provide us with biomarkers of β-cell destruction. This paper is the Chinese translation of Exocytosis protein DOC2B as a biomarker of type 1 diabetes , published on The Journal of Clinical Endocrinology & Metabolism in May 2018 [Aslamy A, Oh E, Ahn M, et al. J Clin Endocrinol Metab, 2018, 103(5): 1966-1976] after obtaining the copyright from the original journal. This study aimed to investigate the changes in the exocytosis protein double C2 domain protein-β (DOC2B) in platelets and islets from T1D humans, pre-diabetic NOD mice, and from T1D patients after islet transplantation. The results showed that the DOC2B protein abundances were substantially reduced in platelets of prediabetic NOD mouse and new-onset T1D patients, while platelet DOC2B levels were increased after islet transplantation in T1D patients. Thus, reduction of DOC2B is an early feature of T1D, and DOC2B abundance may serve as a valuable in vivo indicator of β-cell mass as well as an earlier biomarker of T1D. (Chin J Endocrinol Metab, 2018, 34: 615-622) Key words: DOC2B; Diabetes mellitus, type 1; Blood-derived biomarkers

NCAM2 Fibronectin type-III domains form a rigid structure that binds and activates the Fibroblast Growth Factor Receptor

NCAM1 and NCAM2 have ectodomains consisting of 5 Ig domains followed by 2 membrane-proximal FnIII domains. In this study we investigate and compare the structures and functions of these FnIII domains. The NCAM1 and -2 FnIII2 domains both contain a Walker A motif. In NCAM1 binding of ATP to this motif interferes with NCAM1 binding to FGFR. We obtained a structural model of the NCAM2 FnIII2 domain by NMR spectroscopy, and by titration with an ATP analogue we show that the NCAM2 Walker A motif does not bind ATP. Small angle X-ray scattering (SAXS) data revealed that the NCAM2 FnIII1-2 double domain exhibits a very low degree of flexibility. Moreover, recombinant NCAM2 FnIII domains bind FGFR in vitro, and the FnIII1-2 double domain induces neurite outgrowth in a concentration-dependent manner through activation of FGFR. Several synthetic NCAM1-derived peptides induce neurite outgrowth via FGFR. Only 2 of 5 peptides derived from similar regions in NCAM2 induce neurite outgrowth, but the most potent of these peptides stimulates neurite outgrowth through FGFR-dependent activation of the Ras-MAPK pathway. These results reveal that the NCAM2 FnIII domains form a rigid structure that binds and activates FGFR in a manner related to, but different from NCAM1.

The Cauchy Integral Formula, Quadrature Domains, and Riemann Mapping Theorems

It is well known that a domain in the plane is a quadrature domain with respect to area measure if and only if the function z extends meromorphically to the double, and it is a quadrature domain with respect to boundary arc length measure if and only if the complex unit tangent vector function T(z) extends meromorphically to the double. By applying the Cauchy integral formula to $$\bar{z}$$ , we will shed light on the density of area quadrature domains among smooth domains with real analytic boundary. By extending $$\bar{z}$$ and T(z) and applying the Cauchy integral formula to the Szegő kernel, we will obtain conformal mappings to nearby arc length quadrature domains and even domains that are like the unit disc in that they are simultaneously area and arc length quadrature domains. These “double quadrature domains” can be thought of as analogs of the unit disc in the multiply connected setting and the mappings so obtained as generalized Riemann mappings. The main theorems of this paper are not new, but the methods used in their proofs are new and more constructive than previous methods. The new computational methods give rise to numerical methods for computing generalized Riemann maps to nearby quadrature domains.

Galerkin-collocation domain decomposition method for arbitrary binary black holes

We present a new computational framework for the Galerkin-collocation method for double domain in the context of ADM 3+1 approach in numerical relativity. This work enables us to perform high resolution calculations for initial sets of two arbitrary black holes. We use the Bowen-York method for binary systems and the puncture method to solve the Hamiltonian constraint. The nonlinear numerical code solves the set of equations for the spectral modes using the standard Newton-Raphson method, LU decomposition and Gaussian quadratures. We show convergence of our code for the conformal factor and the ADM mass. Thus, we display features of the conformal factor for different masses, spins and linear momenta.

SNT-1 Functions as the Ca2+ Sensor for Tonic and Evoked Neurotransmitter Release in Caenorhabditis Elegans.

Synaptotagmin-1 (Syt1) binds Ca2+ through its tandem C2 domains (C2A and C2B) and triggers Ca2+-dependent neurotransmitter release. Here, we show that snt-1, the homolog of mammalian Syt1, functions as the Ca2+ sensor for both tonic and evoked neurotransmitter release at the Caenorhabditis elegans neuromuscular junction. Mutations that disrupt Ca2+ binding in double C2 domains of SNT-1 significantly impaired tonic release, whereas disrupting Ca2+ binding in a single C2 domain had no effect, indicating that the Ca2+ binding of the two C2 domains is functionally redundant for tonic release. Stimulus-evoked release was significantly reduced in snt-1 mutants, with prolonged release latency as well as faster rise and decay kinetics. Unlike tonic release, evoked release was triggered by Ca2+ binding solely to the C2B domain. Moreover, we showed that SNT-1 plays an essential role in the priming process in different subpopulations of synaptic vesicles with tight or loose coupling to Ca2+ entry.SIGNIFICANCE STATEMENT We showed that SNT-1 in Caenorhabditis elegans regulates evoked neurotransmitter release through Ca2+ binding to its C2B domain in a similar way to Syt1 in the mouse CNS and the fly neuromuscular junction. However, the largely decreased tonic release in snt-1 mutants argues SNT-1 has a clamping function. Indeed, Ca2+-binding mutations in the C2 domains in SNT-1 significantly reduced the frequency of the miniature EPSC, indicating that SNT-1 also acts as a Ca2+ sensor for tonic release. Therefore, revealing the differential mechanisms between invertebrates and vertebrates will provide significant insights into our understanding how synaptic vesicle fusion is regulated.

Double domain polyethylenimine-based nanoparticles for integrin receptor mediated delivery of plasmid DNA

The objective of the present study is to conjugate L-thyroxine PEI derivative onto another PEI to compensate the amine content of the whole structure which has been utilized for the ligand conjugation. Since αvβ3 integrin receptors are over-expressed on cancer cells and there is binding site for L-thyroxine on these receptors, PEI conjugation by L-thyroxine along with restoring the PEI amine content might be an efficient strategy for targeted delivery using polymeric nanoparticles. The results demonstrated the ability of the PEI conjugate in the formation of nanoparticles with the size of around 210 nm with higher buffering capacity. The conjugated PEI derivative increased the transfection efficiency in the cell lines over-expressing integrin by up to two folds higher than unmodified PEI, whereas in the cell lines lacking the integrin receptors there was no ligand conjugation-associated difference in gene transfer ability. The specificity of transfection demonstrated the delivery of plasmid DNA through integrin receptors. Also, the results of in vivo imaging of the polyplexes revealed that 99mTc-labeled PEI/plasmid DNA complexes accumulated in kidney and bladder 4 h post injection. Therefore, this PEI derivative could be considered as an efficient targeted delivery system for plasmid DNA.

Domain imaging across the magneto-structural phase transitions in Fe1+yTe

The investigation of the magnetic phase transitions in the parent compounds of Fe-based superconductors is regarded essential for an understanding of the pairing mechanism in the related superconducting compounds. Even though the chemical and electronic properties of these materials are often strongly inhomogeneous on a nanometer length scale, studies of the magnetic phase transitions using spatially resolved experimental techniques are still scarce. Here, we present a real space spin-resolved scanning tunneling microscopy investigation of the surface of Fe1+yTe single crystals with different excess Fe content, y, which are continuously driven through the magnetic phase transition. For Fe1.08Te, the transition into the low-temperature monoclinic phase is accompanied by the appearance of a chevron-patterned structural ordering due to the four 90° rotational domains of the monoclinic lattice. Each of the structural domains contains locally commensurate nanoscale diagonal double stripe antiferromagnetic spin order domains with π-phase slips accross domain boundaries. In the low-temperature phase of Fe1.12Te, on the other hand, the chevron pattern gets rather narrow and less well-defined, and an additional 90° rotated component of the spin-order with local plaquette order emerges. The simultaneous imaging of spin and structural order we show here gives valuable insights into the nature of the magneto-structural domains of Fe1+yTe near the tricritical point, which presumably add to the understanding of the mechanism of superconductivity in the related Fe1+yTexSe1−x material.

Doc2b Protects β-Cells Against Inflammatory Damage and Enhances Function.

Loss of functional β-cell mass is an early feature of type 1 diabetes. To release insulin, β-cells require soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes, as well as SNARE complex regulatory proteins like double C2 domain-containing protein β (Doc2b). We hypothesized that Doc2b deficiency or overabundance may confer susceptibility or protection, respectively, to the functional β-cell mass. Indeed, Doc2b+/- knockout mice show an unusually severe response to multiple-low-dose streptozotocin (MLD-STZ), resulting in more apoptotic β-cells and a smaller β-cell mass. In addition, inducible β-cell-specific Doc2b-overexpressing transgenic (βDoc2b-dTg) mice show improved glucose tolerance and resist MLD-STZ-induced disruption of glucose tolerance, fasting hyperglycemia, β-cell apoptosis, and loss of β-cell mass. Mechanistically, Doc2b enrichment enhances glucose-stimulated insulin secretion (GSIS) and SNARE activation and prevents the appearance of apoptotic markers in response to cytokine stress and thapsigargin. Furthermore, expression of a peptide containing the Doc2b tandem C2A and C2B domains is sufficient to confer the beneficial effects of Doc2b enrichment on GSIS, SNARE activation, and apoptosis. These studies demonstrate that Doc2b enrichment in the β-cell protects against diabetogenic and proapoptotic stress. Furthermore, they identify a Doc2b peptide that confers the beneficial effects of Doc2b and may be a therapeutic candidate for protecting functional β-cell mass.

Structural basis of DUX4/IGH-driven transactivation

Oncogenic fusions are major drivers in leukemogenesis and may serve as potent targets for treatment. DUX4/IGHs have been shown to trigger the abnormal expression of ERGalt through binding to DUX4-Responsive-Element (DRE), which leads to B-cell differentiation arrest and a full-fledged B-ALL. Here, we determined the crystal structures of Apo- and DNADRE-bound DUX4HD2 and revealed a clamp-like transactivation mechanism via the double homeobox domain. Biophysical characterization showed that mutations in the interacting interfaces significantly impaired the DNA binding affinity of DUX4 homeobox. These mutations, when introduced into DUX4/IGH, abrogated its transactivation activity in Reh cells. More importantly, the structure-based mutants significantly impaired the inhibitory effects of DUX4/IGH upon B-cell differentiation in mouse progenitor cells. All these results help to define a key DUX4/IGH-DRE recognition/step in B-ALL.

'1H, 13C and 15N Chemical shift assignment for double stranded RNA Binding Domain 1 of Trans Activation Response element (TAR) RNA Binding protein 2'

'1H, 13C and 15N Chemical shift assignment for double stranded RNA Binding Domain 1 of Trans Activation Response element (TAR) RNA Binding protein 2'

Exocytosis Protein DOC2B as a Biomarker of Type 1 Diabetes.

Efforts to preserve β-cell mass in the preclinical stages of type 1 diabetes (T1D) are limited by few blood-derived biomarkers of β-cell destruction. Platelets are proposed sources of blood-derived biomarkers for a variety of diseases, and they show distinct proteomic changes in T1D. Thus, we investigated changes in the exocytosis protein, double C2 domain protein-β (DOC2B) in platelets and islets from T1D humans, and prediabetic nonobese diabetic (NOD) mice. Protein levels of DOC2B were assessed in platelets and islets from prediabetic NOD mice and humans, with and without T1D. Seventeen new-onset T1D human subjects (10.3 ± 3.8 years) were recruited immediately following diagnosis, and platelet DOC2B levels were compared with 14 matched nondiabetic subjects (11.4 ± 2.9 years). Furthermore, DOC2B levels were assessed in T1D human pancreatic tissue samples, cytokine-stimulated human islets ex vivo, and platelets from T1D subjects before and after islet transplantation. DOC2B protein abundance was substantially reduced in prediabetic NOD mouse platelets, and these changes were mirrored in the pancreatic islets from the same mice. Likewise, human DOC2B levels were reduced over twofold in platelets from new-onset T1D human subjects, and this reduction was mirrored in T1D human islets. Cytokine stimulation of normal islets reduced DOC2B expression ex vivo. Remarkably, platelet DOC2B levels increased after islet transplantation in patients with T1D. Reduction of DOC2B is an early feature of T1D, and DOC2B abundance may serve as a valuable in vivo indicator of β-cell mass and an early biomarker of T1D.

Relaxation to Negative Temperatures in Double Domain Systems.

The engineering of quantum systems and their environments has led to our ability now to design composite or complex systems with the properties one desires. In fact, this allows us to couple two or more distinct systems to the same environment where potentially unusual behavior and dynamics can be exhibited. In this Letter we investigate the relaxation of two giant spins or collective spin ensembles individually coupled to the same reservoir. We find that, depending on the configuration of the two individual spin ensembles, the steady state of the composite system does not necessarily reach the ground state of the individual systems, unlike what one would expect for independent environments. Further, when the size of one individual spin ensemble is much larger than the second, collective relaxation can drive the second system to an excited steady state even when it starts in the ground state; that is, the second spin ensemble relaxes towards a negative-temperature steady state.

Deciphering Binding Capabilities of Human Antibodies to Defined Patterns of Antigens

Human antibodies in the families IgG and IgM are highly competent binders utilized by the immune system. The molecules in their monomeric form are capable of forming bivalent binding due to the nature of the double Fab domains. Traditionally it has been hard to precisely compare the binding capabilities of the different IgGs. Here we present a comprehensive study building on a new method where molecularly precise nanoscale patterns of antigens are presented using DNA orgami immobilized in an SPR setup. Variants of human IgG1, 2, 3, 4 and IgM bearing the exact same ligand binding domains are compared and the binding analyzed with respect to both distance between antigens and arrangements of multimeric antigen patterns. These results might have implications for exact nanoscale arrangement of antibodies on biological functions and their relation to complement pathway activation and antibody dependent cellular cytotoxicity is discussed.