Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase

The enzymatic breakdown of sphingomyelin by sphingomyelinases is considered the major source of the second messenger ceramide. Studies on the contribution of the various described acidic and neutral sphingomyelinases to the signaling pool of ceramide have been hampered by the lack of molecular data on the neutral sphingomyelinases (nSMases). We recently identified a mammalian nSMase, an integral membrane protein with remote similarity to bacterial sphingomyelinases. However, its ubiquitous expression pattern is in contrast to previous findings that sphingomyelinase activity is found mainly in brain tissues. By using an improved database search method, combined with phylogenetic analysis, we identified a second mammalian nSMase (nSMase2) with predominant expression in the brain. The sphingomyelinase activity of nSMase2 has a neutral pH optimum, depends on Mg(2+) ions, and is activated by unsaturated fatty acids and phosphatidylserine. Immunofluorescence reveals a neuron-specific punctate perinuclear staining, which colocalizes with a Golgi marker in a number of cell lines. The likely identity of nSMase2 with cca1, a rat protein involved in contact inhibition of 3Y1 fibroblasts, suggests a role for this enzyme in cell cycle arrest. Both mammalian nSMases are members of a superfamily of Mg(2+)-dependent phosphohydrolases, which also contains nucleases, inositol phosphatases, and bacterial toxins.

A fluorescence resonance energy transfer-derived structure of a quantum dot-protein bioconjugate nanoassembly

The first generation of luminescent semiconductor quantum dot (QD)-based hybrid inorganic biomaterials and sensors is now being developed. It is crucial to understand how bioreceptors, especially proteins, interact with these inorganic nanomaterials. As a model system for study, we use Rhodamine red-labeled engineered variants of Escherichia coli maltose-binding protein (MBP) coordinated to the surface of 555-nm emitting CdSe-ZnS core-shell QDs. Fluorescence resonance energy transfer studies were performed to determine the distance from each of six unique MBP-Rhodamine red dye-acceptor locations to the center of the energy-donating QD. In a strategy analogous to a nanoscale global positioning system determination, we use the intraassembly distances determined from the fluorescence resonance energy transfer measurements, the MBP crystallographic coordinates, and a least-squares approach to determine the orientation of the MBP relative to the QD surface. Results indicate that MBP has a preferred orientation on the QD surface. The refined model is in agreement with other evidence, which indicates coordination of the protein to the QD occurs by means of its C-terminal pentahistidine tail, and the size of the QD estimated from the model is in good agreement with physical measurements of QD size. The approach detailed here may be useful in determining the orientation of proteins in other hybrid protein-nanoparticle materials. To our knowledge, this is the first structural model of a hybrid luminescent QD-protein receptor assembly elucidated by using spectroscopic measurements in conjunction with crystallographic and other data.

Glucose-6-Phosphate Dehydrogenase: Update and Analysis of New Mutations around the World

Glucose-6-phosphate dehydrogenase (G6PD) is a key regulatory enzyme in the pentose phosphate pathway which produces nicotinamide adenine dinucleotide phosphate (NADPH) to maintain an adequate reducing environment in the cells and is especially important in red blood cells (RBC). Given its central role in the regulation of redox state, it is understandable that mutations in the gene encoding G6PD can cause deficiency of the protein activity leading to clinical manifestations such as neonatal jaundice and acute hemolytic anemia. Recently, an extensive review has been published about variants in the g6pd gene; recognizing 186 mutations. In this work, we review the state of the art in G6PD deficiency, describing 217 mutations in the g6pd gene; we also compile information about 31 new mutations, 16 that were not recognized and 15 more that have recently been reported. In order to get a better picture of the effects of new described mutations in g6pd gene, we locate the point mutations in the solved three-dimensional structure of the human G6PD protein. We found that class I mutations have the most deleterious effects on the structure and stability of the protein.

Amino-acid sequence of rabbit skeletal tropomyosin and its coiled-coil structure

A tentative amino-acid sequence for the COOH-terminal half of rabbit skeletal tropomyosin is reported. These studies confirm our previous conclusions that this tropomyosin consists of several different but similar polypeptide chains. In the sequence, nonpolar residues occur in two series at intervals of seven residues. Amino-acid residues in series I are three residues on the NH(2)-terminal side of, and four residues on the COOH-terminal side of, residues in series II. The presence of occasional charged or ambivalent residues in the positions of series I or II does not lead to a disruption of this long-range pattern. The majority of residues located between the nonpolar residues are charged or polar amino acids. Two highly similar or identical alpha-helices with the reported sequence can be packed together in parallel in a coiled-coil structure. These may be in register or staggered by seven residues or some multiple of it. The observation that groups of small hydrophobic side chains appear to alternate with groups of bulky side chains suggests that a staggered arrangement of the two alpha-helices would maximize the regularity and hydrophobic interactions of the coiled-coil. Model building considerations show that this would occur with a stagger of 14 residues. Such an arrangement could account for the end-to-end aggregation of tropomyosin in solution, and in crystal and tactoid filaments. However, a structure in which the two polypeptides are in register cannot be ruled out.

Identification of protein biochemical functions by similarity search using the molecular surface database eF-site

The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.

Crystal structure of a clip-domain serine protease and functional roles of the clip domains

Clip-domain serine proteases (SPs) are the essential components of extracellular signaling cascades in various biological processes, especially in embryonic development and the innate immune responses of invertebrates. They consist of a chymotrypsin-like SP domain and one or two clip domains at the N-terminus. Prophenoloxidase-activating factor (PPAF)-II, which belongs to the noncatalytic clip-domain SP family, is indispensable for the generation of the active phenoloxidase leading to melanization, a major defense mechanism of insects. Here, the crystal structure of PPAF-II reveals that the clip domain adopts a novel fold containing a central cleft, which is distinct from the structures of defensins with a similar arrangement of cysteine residues. Ensuing studies demonstrated that PPAF-II forms a homo-oligomer upon cleavage by the upstream protease and that the clip domain of PPAF-II functions as a module for binding phenoloxidase through the central cleft, while the clip domain of a catalytically active easter-type SP plays an essential role in the rapid activation of its protease domain.

Human sulfatases: a structural perspective to catalysis

The sulfatase family of enzymes catalyzes hydrolysis of sulfate ester bonds of a wide variety of substrates. Seventeen genes have been identified in this class of sulfatases, many of which are associated with genetic disorders leading to reduction or loss of function of the corresponding enzymes. Amino acid sequence homology suggests that the enzymes have similar overall folds, mechanisms of action, and bivalent metal ion-binding sites. A catalytic cysteine residue, strictly conserved in prokaryotic and eukaryotic sulfatases, is post-translationally modified into a formylglycine. Hydroxylation of the formylglycine residue by a water molecule forming the activated hydroxylformylglycine (a formylglycine hydrate or a gem-diol) is a necessary step for the enzyme's sulfatase activity. Crystal structures of three human sulfatases, arylsulfatases A and B(ARSA and ARSB), and estrone/dehydroepiandrosterone sulfatase or steroid sulfatase (STS), also known as arylsulfatase C, have been determined. While ARSA and ARSB are water-soluble enzymes, STS has a hydrophobic domain and is an integral membrane protein of the endoplasmic reticulum. In this article, we compare and contrast sulfatase structures and revisit the proposed catalytic mechanism in light of available structural and functional data. Examination of the STS active site reveals substrate-specific interactions previously identified as the estrogen-recognition motif. Because of the proximity of the catalytic cleft of STS to the membrane surface, the lipid bilayer has a critical role in the constitution of the active site, unlike other sulfatases.

Three-dimensional carbon nanotube sponge-array architectures with high energy dissipation

Carbon nanotube sponges and aligned arrays are seamlessly integrated into numerous possible configurations such as series, parallel, package, and sandwich complex structures, leading to significantly broadened stress plateau and enhanced energy dissipation.

Synthesis, Characterization, and Three-Dimensional Structure Generation of Zinc Oxide-Based Nanomedicine for Biomedical Applications

Zinc oxide (ZnO) nanoparticles have been studied as metal-based drugs that may be used for biomedical applications due to the fact of their biocompatibility. Their physicochemical properties, which depend on synthesis techniques involving physical, chemical, biological, and microfluidic reactor methods affect biological activity in vitro and in vivo. Advanced tool-based physicochemical characterization is required to identify the biological and toxicological effects of ZnO nanoparticles. These nanoparticles have variable morphologies and can be molded into three-dimensional structures to enhance their performance. Zinc oxide nanoparticles have shown therapeutic activity against cancer, diabetes, microbial infection, and inflammation. They have also shown the potential to aid in wound healing and can be used for imaging tools and sensors. In this review, we discuss the synthesis techniques, physicochemical characteristics, evaluation tools, techniques used to generate three-dimensional structures, and the various biomedical applications of ZnO nanoparticles.

3D-0D Graphene-Fe3O4 Quantum Dot Hybrids as High-Performance Anode Materials for Sodium-Ion Batteries

Transition metal oxides can be considered as appealing candidates for sodium ion battery anode materials because these low-cost materials possess high capacity and enhanced safety. However, the practical application of these materials is usually limited by their low electronic conductivity and serious volume change during the charging-discharging process. Herein, we report the fabrication of 3D-0D graphene-Fe₃O₄ quantum dot hybrids by a facile one-pot hydrothermal approach as anode materials for sodium-ion batteries. Fe₃O₄ quantum dots with an average size of 4.9 nm are anchored on the surface of 3D structured graphene nanosheets homogeneously. Such unique hierarchical structure are advantageous for enlarging the electrode/electrolyte interface area and enhancing the electrochemical activity of the hybrid materials, inhibiting particle aggregation of Fe₃O₄ and accommodating their volume change during the charging-discharging process as well as enabling fast diffusion of electrons and rapid transfer of electrolyte ions. Consequently, the 3D-0D graphene-Fe₃O₄ quantum dot hybrids exhibit ultrahigh sodium storage capacity (525 mAh g^-1 at 30 mA g^-1), outstanding cycling stability (312 mAh g^-1 after 200 cycles at 50 mA g^-1) and superior rate performance (56 mAh g^-1 at 10 A g^-1).

Mechanism, Structure, and Inhibition of O-GlcNAc Processing Enzymes

The post-translational modification of nucleocytoplasmic proteins with O-linked 2-acetamido-2-deoxy-d-glucopyranose (O-GlcNAc) is a topic of considerable interest and attracts a great deal of research effort. O-GlcNAcylation is a dynamic process which can occur multiple times over the lifetime of a protein, sometimes in a reciprocal relationship with phosphorylation. Several hundred proteins, which are involved in a diverse range of cellular processes, have been identified as being modified with the monosaccharide. The control of the O-GlcNAc modification state on different protein targets appears to be important in the aetiology of a number of diseases, including type II diabetes, neurodegenerative diseases and cancer. Two enzymes are responsible for the addition and removal of the O-GlcNAc modification: uridine diphospho-N-acetylglucosamine:polypeptide beta-N-acetylglucosaminyltransferase (OGT) and O-GlcNAcase (OGA), respectively. Over the past decade the volume of information known about these two enzymes has increased significantly. In particular, mechanistic studies of OGA, in conjunction with structural studies of bacterial homologues of OGA have stimulated the design of inhibitors and offered a rationale for the binding of certain potent and selective inhibitors. Mechanistic information about OGT lags a little way behind OGA, but the recent deduction of the structure of an OGT bacterial homologue should now drive these studies forward.

Structural studies of bacteriophage alpha3 assembly

Bacteriophage alpha3 is a member of the Microviridae, a family of small, single-stranded, icosahedral phages that include phiX174. These viruses have an ssDNA genome associated with approximately 12 copies of an H pilot protein and 60 copies of a small J DNA-binding protein. The surrounding capsid consists of 60 F coat proteins decorated with 12 pentameric spikes of G protein. Assembly proceeds via a 108S empty procapsid that requires the external D and internal B scaffolding proteins for its formation. The alpha3 "open" procapsid structural intermediate was determined to 15A resolution by cryo-electron microscopy (cryo-EM). Unlike the phiX174 "closed" procapsid and the infectious virion, the alpha3 open procapsid has 30A wide pores at the 3-fold vertices and 20A wide gaps between F pentamers as a result of the disordering of two helices in the F capsid protein. The large pores are probably used for DNA entry and internal scaffolding protein exit during DNA packaging. Portions of the B scaffolding protein are located at the 5-fold axes under the spike and in the hydrophobic pocket on the inner surface of the capsid. Protein B appears to have autoproteolytic activity that cleaves at an Arg-Phe motif and probably facilitates the removal of the protein through the 30A wide pores. The structure of the alpha3 mature virion was solved to 3.5A resolution by X-ray crystallography and was used to interpret the open procapsid cryo-EM structure. The main differences between the alpha3 and phiX174 virion structures are in the spike and the DNA-binding proteins. The alpha3 pentameric spikes have a rotation of 3.5 degrees compared to those of phiX174. The alpha3 DNA-binding protein, which is shorter by 13 amino acid residues at its amino end when compared to the phiX174 J protein, retains its carboxy-terminal-binding site on the internal surface of the capsid protein. The icosahedrally ordered structural component of the ssDNA appears to be substantially increased in alpha3 compared to phiX174, allowing the building of about 10% of the ribose-phosphate backbone.

Molecular dynamics simulation in virus research

Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique.

Conformation of lysine vasopressin: a comparison with oxytocin

Starting with assignments of proton nuclear magnetic resonance previously made for oxytocin in deuterated dimethylsulfoxide at 220 MHz, we have assigned resonances for the mammalian antidiuretic hormone, lysine vasopressin. The results demonstrate that spectral assignments of neurohypophyseal hormones and their congeners can, within certain limits, be derived from each other. Comparison of the spectra of lysine vasopressin and oxytocin suggests that the gross backbone conformations of their 20-membered ring components are for the most part similar in deuterated dimethylsulfoxide, whereas the C-terminal acyclic amino-acid sequence of lysine vasopressin is more flexible than that of oxytocin.

Conformational energy studies of oxytocin and its cyclic moiety

Conformational energies were calculated for oxytocin in water, starting with a conformation proposed from nuclear magnetic resonance measurements in [U-(2)H](CH(3))(2)SO. Calculations on the isolated ring showed that conformations with one transannular hydrogen bond had the same energies as those without such bonds; those with two such hydrogen bonds do not appear to form. Calculations on the whole molecule also indicated the existence of several low-energy minima in the energy surface, and no preference for hydrogen-bond formation in the cyclic moiety; the hydrogen bond proposed between the Gly peptide NH and the Cys-6 C=O in the acyclic moiety can form. The proposed proximity of the tail to the ring is one of two low-energy conformations found. The Tyr side chain had two conformations of comparable energy, one over the ring between the Gln and Asn side chains, and the other with the Tyr side chain away from the ring. The oxytocin molecule appears to be flexible, and is probably sensitive to changes in its environment.

3D Analysis of HCMV Induced-Nuclear Membrane Structures by FIB/SEM Tomography: Insight into an Unprecedented Membrane Morphology

We show that focused ion beam/scanning electron microscopy (FIB/SEM) tomography is an excellent method to analyze the three-dimensional structure of a fibroblast nucleus infected with human cytomegalovirus (HCMV). We found that the previously described infoldings of the inner nuclear membrane, which are unique among its kind, form an extremely complex network of membrane structures not predictable by previous two-dimensional studies. In all cases they contained further invaginations (2nd and 3rd order infoldings). Quantification revealed 5498HCMV capsids within two nuclear segments, allowing an estimate of 15,000 to 30,000 capsids in the entire nucleus five days post infection. Only 0.8% proved to be enveloped capsids which were exclusively detected in 1st order infoldings (perinuclear space). Distribution of the capsids between 1st, 2nd and 3rd order infoldings is in complete agreement with the envelopment/de-envelopment model for egress of HCMV capsids from the nucleus and we confirm that capsid budding does occur at the large infoldings. Based on our results we propose the pushing membrane model: HCMV infection induces local disruption of the nuclear lamina and synthesis of new membrane material which is pushed into the nucleoplasm, forming complex membrane infoldings in a highly abundant manner, which then may be also used by nucleocapsids for budding.

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.

Characterization of anti-anti-idiotypic antibodies that bind antigen and an anti-idiotype

Two mouse monoclonal anti-anti-idiotopic antibodies (anti-anti-Id, Ab3), AF14 and AF52, were prepared by immunizing BALB/c mice with rabbit polyclonal anti-idiotypic antibodies (anti-Id, Ab2) raised against antibody D1.3 (Ab1) specific for the antigen hen egg lysozyme. AF14 and AF52 react with an "internal image" monoclonal mouse anti-Id antibody E5.2 (Ab2), previously raised against D1.3, with affinity constants (1.0 x 10(9) M-1 and 2.4 x 10(7) M-1, respectively) usually observed in secondary responses against protein antigens. They also react with the antigen but with lower affinity (1.8 x 10(6) M-1 and 3.8 x 10(6) M-1). This pattern of affinities for the anti-Id and for the antigen also was displayed by the sera of the immunized mice. The amino acid sequences of AF14 and AF52 are very close to that of D1.3. In particular, the amino acid side chains that contribute to contacts with both antigen and anti-Id are largely conserved in AF14 and AF52 compared with D1.3. Therapeutic immunizations against different pathogenic antigens using anti-Id antibodies have been proposed. Our experiments show that a response to an anti-Id immunogen elicits anti-anti-Id antibodies that are optimized for binding the anti-Id antibodies rather than the antigen.

The structure of spider toxin huwentoxin-II with unique disulfide linkage: evidence for structural evolution

The three-dimensional structure of huwentoxin-II (HWTX-II), an insecticidal peptide purified from the venom of spider Selenocosmia huwena with a unique disulfide bond linkage as I-III, II-V, and IV-VI, has been determined using 2D (1)H-NMR. The resulting structure of HWTX-II contains two beta-turns (C4-S7 and K24-W27) and a double-stranded antiparallel beta-sheet (W27-C29 and C34-K36). Although the C-terminal double-stranded beta-sheet cross-linked by two disulfide bonds (II-V and IV-VI in HWTX-II, II-V and III-VI in the ICK molecules) is conserved both in HWTX-II and the ICK molecules, the structure of HWTX-II is unexpected absence of the cystine knot because of its unique disulfide linkage. It suggests that HWTX-II adopts a novel scaffold different from the ICK motif that is adopted by all other spider toxin structures elucidated thus far. Furthermore, the structure of HWTX-II, which conforms to the disulfide-directed beta-hairpin (DDH) motif, not only supports the hypothesis that the ICK is a minor elaboration of the more ancestral DDH motif but also suggests that HWTX-II may have evolved from the same structural ancestor.

Method for correlation of proton magnetic resonance assignments in different solvents: conformational transition of oxytocin and lysine vasopressin from dimethylsulfoxide to water

The peptide amide, primary carboxamide, and aromatic proton resonances were assigned to specific hydrogens of oxytocin and lysine vasopressin (Lys-VP) in water at 23 degrees at pH 2.5 and 4.2, respectively. We started with the spectral assignments of oxytocin and Lys-VP determined in deuterated dimethylsulfoxide (Me(2)SO) and monitored the course of each of these resonances as the proportion of water to Me(2)SO was gradually increased. Changes in each of the two hormones in chemical shifts and in some coupling constants indicate that conformational alterations occur in both oxytocin and Lys-VP during the solvent transition from Me(2)SO to water. This study is a specific application of a general method for correlating spectral assignments in different solvents and for monitoring conformational changes accompanying solvent transitions. Application of this technique requires only that the solvent components be miscible over the entire transitional range, that spectral changes of the solute be simple enough to follow, and that the associated structural changes of the solute be "rapid on the proton magnetic resonance time-scale."

Anisotropic Nanocellulose Aerogel Loaded with Modified UiO-66 as Efficient Adsorbent for Heavy Metal Ions Removal

Currently, the preparation of outstanding adsorbents has attracted public concern in environmentally friendly and sustainable pollutant redress. Herein, we report a directional freeze-drying method to prepare a strong and reusable adsorbent by introducing metal-organic framework which modified by ethylene diamine tetraacetic acid (named UiO-66-EDTA) into cellulose nanofiber (CNF) aerogel. Compared to traditional aerogels, the fabricated adsorbent showed a good flexibility and reusability by forming a homogeneous three-dimensional structure. By controlling the concentration of a crosslinkable carboxymethyl cellulose (CMC) solution, we produced aerogels with different pore structures and fibrillar, columnar, and lamellar morphologies. The obtained UiO-66-EDTA/CNF/CMC aerogel (U_-EDTACCA) showed an excellent adsorption performance for a total of nine types of heavy metal ions, as the removal efficiency could reach 91%. Moreover, the aerogels could retain 88% of their original shape after five cycles. The aerogel may be an appropriate material for the adsorption of heavy metal ions.

Silver Nanoparticle-Doped 3D Porous Carbon Nanofibers as Separator Coating for Stable Lithium Metal Anodes

The ever-increasing demand for electric devices and vehicles prompts the fast development of energy storage systems. Lithium metal is thought to be the most promising electrode for high-performance batteries. However, the growth of lithium dendrites impedes the industrial production of lithium metal batteries. Herein, an effective approach is proposed by coating a commercial separator with three-dimensional porous carbon fibers loaded with silver nanoparticles (Ag-PCNFs), which can be regarded as a subsidiary of the electrode to improve the cycling performance of lithium metal batteries. The porous structure with a high specific surface area endows the electrode with a high lithium-loading capacity. The silver nanoparticles provide the electrode pro-Li property and excellent electrical conductivity, which are beneficial for the electrochemical reaction and reduce the local current density to attain a dendrite-free electrode. Electrochemical cycling performance of symmetric Li-Li batteries shows that Ag-PCNF coating can hinder dendrite growth and enhance the cycling stability, indicating that Ag-PCNFs acting as host materials can effectively guide the deposition of Li and solve the dendrite problem.

Animal NLRs provide structural insights into plant NLR function

BACKGROUND

The plant immune system employs intracellular NLRs (nucleotide binding [NB], leucine-rich repeat [LRR]/nucleotide-binding oligomerization domain [NOD]-like receptors) to detect effector proteins secreted into the plant cell by potential pathogens. Activated plant NLRs trigger a range of immune responses, collectively known as the hypersensitive response (HR), which culminates in death of the infected cell. Plant NLRs show structural and functional resemblance to animal NLRs involved in inflammatory and innate immune responses. Therefore, knowledge of the activation and regulation of animal NLRs can help us understand the mechanism of action of plant NLRs, and vice versa.

SCOPE

This review provides an overview of the innate immune pathways in plants and animals, focusing on the available structural and biochemical information available for both plant and animal NLRs. We highlight the gap in knowledge between the animal and plant systems, in particular the lack of structural information for plant NLRs, with crystal structures only available for the N-terminal domains of plant NLRs and an integrated decoy domain, in contrast to the more complete structures available for animal NLRs. We assess the similarities and differences between plant and animal NLRs, and use the structural information on the animal NLR pair NAIP/NLRC4 to derive a plausible model for plant NLR activation.

CONCLUSIONS

Signalling by cooperative assembly formation (SCAF) appears to operate in most innate immunity pathways, including plant and animal NLRs. Our proposed model of plant NLR activation includes three key steps: (1) initially, the NLR exists in an inactive auto-inhibited state; (2) a combination of binding by activating elicitor and ATP leads to a structural rearrangement of the NLR; and (3) signalling occurs through cooperative assembly of the resistosome. Further studies, structural and biochemical in particular, will be required to provide additional evidence for the different features of this model and shed light on the many existing variations, e.g. helper NLRs and NLRs containing integrated decoys.

Three-Dimensional Graphene Hydrogel Decorated with SnO2 for High-Performance NO2 Sensing with Enhanced Immunity to Humidity

A facile, one-step hydrothermal route was exploited to prepare SnO₂-decorated reduced graphene oxide hydrogel (SnO₂/RGOH) with three-dimensional (3D) porous structures for NO₂ gas detection. Various material characterizations demonstrate the effective deoxygenation of graphene oxide and in situ growth of rutile SnO₂ nanoparticles (NPs) on 3D RGOH. Compared with the pristine RGOH, the SnO₂/RGOH displayed much lower limit of detection (LOD) and an order of magnitude higher sensitivity, revealing the distinct impact of SnO₂ NPs in improving the NO₂-sensing properties. An exceptional low theoretical LOD of 2.8 ppb was obtained at room temperature. The p-n heterojunction formed at the interface between RGOH and SnO₂ facilitates the charge transfer, improving both the sensitivity in NO₂ detection and the conductivity of hybrid material. Considering that existing SnO₂/RGO-based NO₂ sensors suffer from great vulnerability to humidity, here we employed integrated microheaters to effectively suppress the response to humidity, with nearly unimpaired response to NO₂, which boosted the selectivity. Notably, a flexible NO₂ sensor was constructed on a liquid crystal polymer substrate with endurance to mechanical deformation. This work indicates the feasibility of optimizing the gas-sensing performance of sensors by combining rational material hybridization, 3D structural engineering with temperature modulation.

The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway

Mycobacterium smegmatis MshC catalyzes the ATP-dependent condensation of GlcN-Ins and l-cysteine to form l-Cys-GlcN-Ins, the penultimate step in mycothiol biosynthesis. Attempts to crystallize the native, full-length MshC have been unsuccessful. However, incubation of the enzyme with the cysteinyl adenylate analogue, 5'-O-[N-(l-cysteinyl)-sulfamonyl]adenosine (CSA), followed by a 24-h limited trypsin proteolysis yielded an enzyme preparation that readily crystallized. The three-dimensional structure of MshC with CSA bound in the active site was solved and refined to 1.6 A. The refined structure exhibited electron density corresponding to the entire 47 kDa MshC molecule, with the exception of the KMSKS loop (residues 285-297), a loop previously implicated in the formation of the adenylate in related tRNA synthases. The overall tertiary fold of MshC is similar to that of cysteinyl-tRNA synthetase, with a Rossmann fold catalytic domain. The interaction of the thiolate of CSA with a zinc ion at the base of the active site suggests that the metal ion participates in amino acid binding and discrimination. A number of active site residues were observed to interact with the ligand, suggesting a role in substrate binding and catalysis. Analysis utilizing modeling of the proteolyzed loop and GlcN-Ins docking, as well as the examination of sequence conservation in the active site suggests similarities and differences between cysteinyl-tRNA synthetases and MshC in recognition of the substrates for their respective reactions.