Three-dimensional Structural Features Research Articles

The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution.

In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.

Modeling of macromolecular proteins in prophenoloxidase cascade through experimental and computational approaches.

Prophenoloxidase (ProPO) cascade is a principal defense system in crustaceans, which consists of a variety of pattern recognition proteins (lipopolysaccharide and β-glucan-binding protein [β-GBP], β-GBP, and β-glucan recognition protein), proteases (serine protease), and protease inhibitors (α2-macroglobulin and pacifastin) to regulate the protection mechanism in crustaceans. In the prophneoloxidase pathway, the protein-protein interactions (PPIs) and other immune-related analyses still have not been reported. Moreover, the structural features of ProPO cascade proteins have not yet been reported, hence we constructed the three-dimensional structural features for all ProPO pathway proteins. Their PPIs were studied through an in silico approach. Laminarin has been identified as a triggering activator and it showed energetic binding with homology modeled β-GBP and activated the β-GBP, followed by the protein-protein complex formation leading to phenoloxidase synthesis. These findings provided a novel view of the ProPO mechanism and enhanced our knowledge of the innate immune system in crustaceans via computation. In conclusion, we propose a combined experimental and computational approach to analyze the mechanism of ProPO cascade proteins.

Therapeutic Potential of Spirooxindoles as Antiviral Agents.

Antiviral therapeutics with profiles of high potency, low resistance, panserotype, and low toxicity remain challenging, and obtaining such agents continues to be an active area of therapeutic development. Due to their unique three-dimensional structural features, spirooxindoles have been identified as privileged chemotypes for antiviral drug development. Among them, spiro-pyrazolopyridone oxindoles have been recently reported as potent inhibitors of dengue virus NS4B, leading to the discovery of an orally bioavailable preclinical candidate (R)-44 with excellent in vivo efficacy in a dengue viremia mouse model. This review highlights recent advances in the development of biologically active spirooxindoles for their antiviral potential, primarily focusing on the structure-activity relationships (SARs) and modes of action, as well as future directions to achieve more potent analogues toward a viable antiviral therapy.

A New Assessment Method for Structural-Control Failure Mechanisms in Rock Slopes — Case Examples

Mass movement processes of bedrock slopes are highly dependent on the orientations of structural discontinuities within the rock mass. The associated hazards are typically defined by the orientation of structures and associated mechanisms of slope failure such as planar sliding, wedge sliding and toppling. A typical rock mass with multiple weak surfaces, or discontinuities, may form a consistent pattern over a range of spatial scale. The type of hazard resulting from the pattern of discontinuities will vary according to the angle and direction of the slope face. Assessing the risk of rock slope instability involves understanding of the complex three-dimensional structural features of the rock mass. Recent developments in stereographic methods show advantages are gained by representing wedges by linking great circles rather than showing the intersection line on the stereograph. We applied these methods to three rock slopes where active mass movement has occurred. The case studies include a large rock slide-debris avalanche in the Philippines, coastal cliffs in Australia and mining excavation slopes in Ghana, West Africa.

High resolution imaging of acne lesion development and scarring in human facial skin using OCT-based microangiography.

Acne is a common skin disease that often leads to scarring. Collagen and other tissue damage from the inflammation of acne give rise to permanent skin texture and microvascular changes. In this study, we demonstrate the capabilities of optical coherence tomography-based microangiography in detecting high-resolution, three-dimensional structural, and microvascular features of in vivo human facial skin during acne lesion initiation and scar development. A real time swept source optical coherence tomography system is used in this study to acquire volumetric images of human skin. The system operates on a central wavelength of 1,310 nm with an A-line rate of 100 kHz, and with an extended imaging range (∼12 mm in air). The system uses a handheld imaging probe to image acne lesion on a facial skin of a volunteer. We utilize optical microangiography (OMAG) technique to evaluate the changes in microvasculature and tissue structure. Thanks to the high sensitivity of OMAG, we are able to image microvasculature up to capillary level and visualize the remodeled vessels around the acne lesion. Moreover, vascular density change derived from OMAG measurement is provided as an alternative biomarker for the assessment of human skin diseases. In contrast to other techniques like histology or microscopy, our technique made it possible to image 3D tissue structure and microvasculature up to 1.5 mm depth in vivo without the need of exogenous contrast agents. The presented results are promising to facilitate clinical trials aiming to treat acne lesion scarring, as well as other prevalent skin diseases, by detecting cutaneous blood flow and structural changes within human skin in vivo.

Applications of self-assembling peptide scaffolds in regenerative medicine: the way to the clinic.

Peptides that self-assemble into well-defined nanofibrous networks provide a prominent alternative to traditional biomaterials for fabricating scaffolds for use in regenerative medicine and other biomedical applications. Such scaffolds can be generated by decorating a peptide backbone with other bioactives such as cell specific adhesion peptides, growth factors and enzyme cleavable sequences. They can be designed to mimic the three-dimensional (3D) structural features of native ECM and can therefore also provide insight into the ECM-cell interactions needed for development of scaffolds that can serve as regeneration templates for specific target tissues or organs. This review highlights the potential application of self-assembling peptides in regenerative medicine.

Predicting DNA-binding sites of proteins based on sequential and 3D structural information

Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.

Biological features of ultrasound assisted acellular spinal cord scaffold

Objective To observe three-dimensional structure and biological features of rat acellular spinal cord scaffold prepared by sonic oscillation and chemical extraction in order to offer an ideal scaffold for spinal cord tissue engineering research.Methods Rat spinal cord underwent acellular treatment with sonic oscillation and chemical extraction (Triton X-100 at volume fracture of 2％ and sodium deoxycholate at volume fracture of 2％) (acellular spinal cord group).In contrast with spinal cord tissue of normal rats (control group),general morphology,histology and ultramicro three-dimensional structure of acellular spinal cord scaffold were observed and aperture size,factor of porosity,water ratio,enzymolysis ratio and stability in water solution of the scaffold were also detected.Results Acellular spinal cord group showed effective removal of original cell components with factor of porosity for (94.57 ±3.45) ％ and water content for (88.62 ± 1.0) ％,and satisfactory three-dimensional structure with average aperture of 46 μm.Scaffold showed gradual degradation in enzymolysis solution and enzymolysis rate reached (69.03 ± 2.19)％ at 20 hours.Besides,scaffold showed stepwise disintegration in double distilled water and hydrolysis rate was (62.55 ± 1.70) ％ at 8 days.While,normal spinal cord showed close structure,generous neurons and myelin sheath with factor of porosity for (0.04 ± 0.02) ％ and water content for (62.4 ± 1.5) ％,and unobvious pore structure under scanning electron microscope.Normal spinal cord were degraded gradually in enzymolysis solution and enzymolysis rate was (37.62 ± 0.9)％ at 20hours.In the meantime,normal spinal cord were disintegrated gradually in double distilled water and hydrolysis rate was (40.97 ± 0.81) ％ at 8 days.Conclusions Acellular spinal cord scaffold prepared by sonic oscillation plus chemical extraction achieves complete removal of cell components,intact extracellular matrix,and satisfactory results in three-dimensional network structures,factor of porosity and water content.Also,the scaffold meets theoretical demands of tissue-engineered spinal cord scaffold and is an ideal alterative for tissue-engineered spinal cord scaffold. Key words: Spinal cord injuries; Tissue engineering; Sonication; Acellular spinal cord scaffold

Quantitative analysis of mechanically retentive ceramic bracket base surfaces with a three-dimensional imaging system

To investigate the three-dimensional structural features of three types of mechanically retentive ceramic bracket bases. One type of stainless steel (MicroArch, Tomy, Tokyo, Japan) and three types of ceramic maxillary right central incisor brackets-Crystaline MB (Tomy), INVU (TP Orthodontics, La Porte, Ind), and Inspire Ice (Ormco, Glendora, Calif)-were tested to compare and quantitatively analyze differences in the surface features of each ceramic bracket base using scanning electron microscopy (SEM), a three-dimensional (3D) optical surface profiler, and microcomputed tomography (micro-CT). One-way analysis of variance was used to find differences in bracket base surface roughness values and surface areas between groups according to base designs. Tukey's honestly significant differences tests were used for post hoc comparisons. SEM revealed that each bracket exhibited a unique surface texture (MicroArch, double mesh; Crystaline MB, irregular; INVU, single mesh; Inspire Ice, bead ball). With a 3D optical surface profiler, the stainless steel bracket showed significantly higher surface roughness values. Crystaline MB had significantly higher surface roughness values than Inspire Ice. Micro-CT demonstrated that stainless steel brackets showed significantly higher whole and unit bracket base surface areas. Among ceramic brackets, INVU showed significantly higher whole bracket base surface area, and Crystaline MB showed a significantly higher unit bracket base surface area than Inspire Ice. Irregular bracket surface features showed the highest surface roughness values and unit bracket base surface area among ceramic brackets, which contributes to increased mechanically retentive bracket bonding strength.

Poly[[tetraaquadi-μ4-fumarato-μ2-oxalato-dierbium(III)] tetrahydrate

The title compound, {[Er2(C4H2O4)2(C2O4)(H2O)4]·4H2O}n, was synthesized by the reaction of erbium nitrate hexa­hydrate with fumaric acid and oxalic acid under hydro­thermal conditions. The Er3+ cation (site symmetry ..2) is eight-coordinated by six O atoms from four fumarate anions (site symmetry ..2) and one bidentate oxalate anion (site symmetry 222), and by two water mol­ecules. The complex exhibits a three-dimensional structure consisting of oxalate pillared Er–fumarate layers with channels occupied by coordinating and lattice water mol­ecules. The three-dimensional structure features by Owater—H⋯O hydrogen bonds involving both the coordinating and lattice water mol­ecules.

NMR Structural Analysis of MC1R-Targeted Rhenium(I) Metallopeptides and Biological Evaluation of99mTc(I) Congeners

The melanocortin receptor 1 (MC1R) is a specific molecular target for detection and therapy of melanoma, as it is overexpressed in human melanomas. The design of novel peptide-based MC1R-specific probes for imaging or targeted radionuclide therapy is being actively pursued. Aiming to visualize melanoma in vivo by single photon emission computed tomography (SPECT) imaging using 99mTc(CO)3-labeled cyclic melanocyte stimulating hormone analogues, we have designed the novel cyclic peptides c[S-NO2-C6H-CO-His-DPhe-Arg-Trp-Cys]-Lys-NH2 (1) and c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys]-Lys-NH2 (2) and their corresponding conjugates c[S-NO2-C6H3-CO-His-DPhe-Arg-Trp-Cys]-Lys(pz)-NH2 (L1) and c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys]-Lys(pz)-NH2 (L2), which incorporate a pyrazolyl-diamine chelating unit (pz). Upon reaction with adequate organometallic precursors, we prepared the metalated peptides c[S-NO2-C6H3-CO-His-DPhe-Arg-Trp-Cys]-Lys(pz-M(CO)3)-NH2 (M = Re (Re1), Tc (Tc1)) and c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys]-Lys(pz-M(CO)3)-NH2 (M = Re (Re2), Tc (Tc2)). Competitive binding affinity assays demonstrated that metalation of L1 and L2 did not lead to a significant decrease of binding affinity toward MC1R, as concluded by comparing the IC50 values of Re1 (IC50 = 690 ± 250 nM) and Re2 (IC50 = 176 ± 5 nM) to those of the nonmetalated conjugates L1 (IC50 = 430 ± 100 nM) and L2 (IC50 = 179 ± 39 nM). Furthermore, the potency of the alkylamine-bridged peptide derivatives is superior to that of the alkylthioaryl-bridged derivatives. NMR structural analysis performed for 1, L1, and Re1 has shown that the peptide moiety displayed an atypical β-turn conformation in solution. The three-dimensional structural features of the peptide moiety were also conserved upon conjugation to the chelator and, most importantly, after metalation. Despite presenting a significant cell internalization degree and moderate retention in murine melanoma cells, the radiopeptides Tc1 and Tc2 displayed poor tumor-targeting properties in a B16F1 melanoma-bearing mouse model.

Structure of the Nuclear Factor κB-inducing Kinase (NIK) Kinase Domain Reveals a Constitutively Active Conformation

NF-κB-inducing kinase (NIK) is a central component in the non-canonical NF-κB signaling pathway. Excessive NIK activity is implicated in various disorders, such as autoimmune conditions and cancers. Here, we report the first crystal structure of truncated human NIK in complex with adenosine 5'-O-(thiotriphosphate) at a resolution of 2.5 Å. This truncated protein is a catalytically active construct, including an N-terminal extension of 60 residues prior to the kinase domain, the kinase domain, and 20 residues afterward. The structure reveals that the NIK kinase domain assumes an active conformation in the absence of any phosphorylation. Analysis of the structure uncovers a unique role for the N-terminal extension sequence, which stabilizes helix αC in the active orientation and keeps the kinase domain in the catalytically competent conformation. Our findings shed light on the long-standing debate over whether NIK is a constitutively active kinase. They also provide a molecular basis for the recent observation of gain-of-function activity for an N-terminal deletion mutant (ΔN324) of NIK, leading to constitutive non-canonical NF-κB signaling with enhanced B-cell adhesion and apoptosis resistance.

Mesoporous Co3O4 with different porosities as catalysts for the lithium–oxygen cell

Mesoporous cobalt oxides (Co3O4) with different porosities were employed as the electrochemical catalysts of lithium–oxygen batteries. The mesoporous Co3O4 demonstrated significantly improved round-trip efficiency and specific capacity over the bulk catalyst. Moreover, electrochemical measurement results suggest that the highly open and continuous three-dimensional cubic mesoporous structural features of the catalyst are imperative for its much higher catalytic reactivity than the two-dimensional hexagonal mesoporous Co3O4. A capacity close to 2250mAhg−1carbon and a round-trip efficiency of 81.42% were obtained for the mesoporous Co3O4-KIT-6-40 catalyzed air electrode. It is suggested that the mesoporous metal oxide could be a promising catalyst of air electrode for the high performance lithium–oxygen battery.

Conditions and features of matrix and bulk carbonization of the organic precursors

Comparative research of matrix and bulk carbonization of some organic precursors (sucrose, acetonitrile) in silica mesoporous materials SBA-15 and KIT-6 was conducted. X-ray diffraction, nitrogen adsorption analysis, Raman spectroscopy were used for determination of the structural-sorption characteristics of the obtained materials. It was shown that the carbon mesoporous materials CMK-8 obtained in the mesopores of KIT-6 had higher adsorption characteristics because of features of three-dimensional cubic structure, larger pore volume and framework’s wall thickness. It was established that partially graphitized spatially well-organized carbon materials were formed as a result of pyrolysis of acetonitrile in the silica matrices SBA-15 and KIT-6. It was conditioned by the absence of considerable spatial limitations for growth of graphite structures on the initial stage of the synthesis when the pores of the matrix were not filled up with the organic precursor. Product of bulk carbonization of sucrose is compact carbon microporous framework with low sorption characteristics (micropore volume is 0.09 cm3/g).

Poly[[diaquadi-μ2-cyanido-bis(μ2-pyrazine-2-carboxylato)dicopper(I)copper(II)] dihydrate

In the title compound, {[CuIICuI 2(C5H3N2O2)2(CN)2(H2O)2]·2H2O}n, the CuII atom lies on an inversion centre and is octa­hedrally coordinated by two N atoms and two O atoms from opposing pyrazine-2-carboxyl­ate (2-pac) ligands and two water O atoms. The CuI atom has a triangular geometry, coordinated by one N atom and one C atom from two bridging cyanide ligands, and another N atom from the 2-pac ligand. The three-dimensional structure features a succession of two-dimensional sheets containing [Cu(CN)]n chains linked by Cu(2-pac)2(H2O)2 groups. The coordinated and free water mol­ecules are involved in an extended three-dimensional hydrogen-bond network with the 2-pac ligands.

Synthesis, Crystal Structure, and Photoluminescent Properties of Ternary Cd(II)/Triazolate/Chloride System

Solvothermal reactions of cadmium chloride and 1,2,4-triazole (Htrz) in different solvent mediums have successfully synthesized five ternary Cd(II)/trz/Cl(-) complexes, [Cd(trz)Cl]·H(2)O (1·H(2)O), [Cd(4)(trz)(5)Cl(3)(H(2)O)]·(THF)(1.25)·(H(2)O)(2.5) (2·1.25THF·2.5H(2)O), [Cd(3)(trz)(2)Cl(MeCN)] (3), [Cd(3)(trz)(4)Cl(2)]·(H(2)O)(0.5) (4·0.5H(2)O), and [Cd(4)(trz)(6)Cl(2)(H(2)O)(0.5)]·(H(2)O)(3.5) (5·3.5H(2)O). All of these five coordination polymers have three-dimensional (3-D) structural features, which are constructed by distinct substructures including clusters, chains, rings, and even 3-D frameworks. In all cases, 1,2,4-triazolate adopts a μ(1,2,4) bridging mode, and chloride ions display a μ(2), μ(3), μ(4) bridging mode, respectively, which makes the structural diversity in the assembling system, for example, μ(4)-Cl and cadmium triazolate, build up an unprecedented tetranuclear cluster [Cd(4)(trz)(8)Cl](-) in 2. All of the materials exhibit intense blue fluorescent emission and high thermal stability, wherein 1 presents an interesting guest-responsive photoluminescent property.

Identification of Functional Regions Defining Different Activity in Caspase-3 and Caspase-7 within Cells

Caspases are central to apoptosis, and the principal executioner caspases, caspase-3 and -7, were reported to be similar in activity, primary structure, and three-dimensional structure. Here, we identified different activity in caspase-3 and -7 within cells and examined the relationship between their structure and function using human cells expressing almost equal amounts of exogenous caspase-3, caspase-7, and/or chimeric constructs after down-regulation of endogenous caspase-3 and -7 expression. Caspase-3 (produced in human cells) showed much stronger cleaving activity than caspase-7 against a low molecular weight substrate in vitro dependent on four specific amino acid regions. Within cells, however, an additional three regions were required for caspase-3 to exert much stronger protease activity than caspase-7 against cellular substrates. Three of the former four regions and the latter three regions were shown to form two different three-dimensional structures that were located at the interface of the homodimer of procaspase-7 on opposite sides. In addition, procaspase-3 and -7 revealed specific homodimer-forming activity within cells dependent on five amino acid regions, which were included in the regions critical to the cleaving activity within cells. Thus, human caspase-3 and -7 exhibit differences in protease activity, specific homodimer-forming activity, and three-dimensional structural features, all of which are closely interrelated.

Tetrakis(2,2′-bipyridine)-1κ4N,N′;4κ4N,N′-{μ4-N,N′-bis[3-(2-oxidoethylamino)propyl]oxamidato(4−)-1:2:3:4κO:κ3N,N′,O′:κ3O′′,N′′,N′′′:κO′′′}tetracopper(II) tetrakis(perchlorate)

The title complex, [Cu(4)(C(12)H(22)N(4)O(4))(C(10)H(8)N(2))(4)](ClO(4))(4), has a novel tetranuclear copper(II) cation with the oxamidate and ethanolate groups of a trans tetraanion of N,N'-bis[3-(hydroxyethylamino)propyl]oxamide (H(4)heap) as bridges. The Cu...Cu separation through the oxamide group is 5.1592 (15) A, while those through the two ethanolate bridges are 3.3845 (13) and 3.3392 (13) A. The two central copper(II) ions are in square-planar N(2)O(2) environments, while the two terminal copper(II) ions have distorted N(4)O square-pyramidal geometries. The heap(4-) ligand, with an iminoalcohol form, has both an oxamide and two ethanolate bridges. Two of the four perchlorate anions are disordered and have long contacts with the square-planar Cu(II) ions. The three-dimensional structure features arene-perchlorate C-H...O hydrogen bonds and pi-pi stacking.

Subunit–subunit interactions and overall topology of the dimeric mitochondrial ATP synthase of Polytomella sp.

Mitochondrial F 1F 0-ATP synthase of chlorophycean algae is a dimeric complex of 1600 kDa constituted by 17 different subunits with varying stoichiometries, 8 of them conserved in all eukaryotes and 9 that seem to be unique to the algal lineage (subunits ASA1–9). Two different models proposing the topological assemblage of the nine ASA subunits in the ATP synthase of the colorless alga Polytomella sp. have been put forward. Here, we readdressed the overall topology of the enzyme with different experimental approaches: detection of close vicinities between subunits based on cross-linking experiments and dissociation of the enzyme into subcomplexes, inference of subunit stoichiometry based on cysteine residue labelling, and general three-dimensional structural features of the complex as obtained from small-angle X-ray scattering and electron microscopy image reconstruction. Based on the available data, we refine the topological arrangement of the subunits that constitute the mitochondrial ATP synthase of Polytomella sp.

Mixed-ligand coordination polymers constructed from flexible 2,2′-biphenyldicarboxylate and rigid isomeric bipyridines

Six coordination polymers have been synthesized and characterized based on dpa and isomeric bipyridine mixed ligands with various metal ions. Complex 1 exhibits a two-dimensional layer structure. Complex 2 is isomorphic to complex 1, with only small differences in bond lengths and bond angles. Complex 3 shows a one-dimensional chain structure composed of interesting pentanuclear Co building units. Complex 4 possesses a two-dimensional (4, 4) layer network, which crystallizes in a homochiral space group. During the synthesis process of complex 4, the dpa ligands decompose and form 2-bpa ligands, which connect with Ni atoms and produce the two-dimensional complex 5. Complex 6 exhibits a three-dimensional supramolecular structural feature constructed from discrete building units with π–π interactions. Furthermore, the magnetic properties of complex 2 are studied.