Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter.

Visualizing dynamics of kinase activity in living animals is essential for mechanistic understanding of cell and developmental biology. We describe GFP-based kinase reporters that phase-separate upon kinase activation via multivalent protein-protein interactions, forming intensively fluorescent droplets. Called SPARK (separation of phases-based activity reporter of kinase), these reporters have large dynamic range (fluorescence change), high brightness, fast kinetics, and are reversible. The SPARK-based protein kinase A (PKA) reporter reveals oscillatory dynamics of PKA activities upon G protein-coupled receptor activation. The SPARK-based extracellular signal-regulated kinase (ERK) reporter unveils transient dynamics of ERK activity during tracheal metamorphosis in live Drosophila. Because of intensive brightness and simple signal pattern, SPARKs allow easy examination of kinase signaling in living animals in a qualitative way. The modular design of SPARK will facilitate development of reporters of other kinases.

ß-Amyloid Peptides Manipulate Switching Behaviors of Donor-Acceptor Stenhouse Adducts.

Molecular switching plays a critical role in biological and displaying systems. Donor-acceptor Stenhouse adducts (DASAs) is a newly re-discovered series of switchable photochromes, and light is the most used approach to control its switching behavior. In this report, we speculated that hydrophobic binding pockets of biologically relevant peptides/proteins could be harnessed to alter its switching behavior without the assistance of light. We designed and synthesized a DASA compound SHA-2, and we demonstrated that the Aß40 species could stabilize SHA-2 in the linear conformation and decrease the rate of molecular switching via fluorescence spectral studies. Moreover, molecular dynamics simulation revealed that SHA-2 could bind to the hydrophobic fragment of the peptide and resulted in substantial changes in the tertiary structure of Aß40 monomer. This structural change is likely to impede the aggregation of Aß40, as evidenced by the results from thioflavin T fluorescence and ProteoStat aggregation detection experiments. We believe that our study opens a new window to alter the switching behavior of DASA via DASA-peptide/protein interactions.

Designed peptides that assemble into cross-α amyloid-like structures.

Amyloids adopt 'cross-ß' structures composed of long, twisted fibrils with ß-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted ß-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.

Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals.

A family of proteases called caspases mediate apoptosis signaling in animals. We report a GFP-based fluorogenic protease reporter, dubbed "FlipGFP", by flipping a beta strand of the GFP. Upon protease activation and cleavage, the beta strand is restored, leading to reconstitution of the GFP and fluorescence. FlipGFP-based TEV protease reporter achieves 100-fold fluorescence change. A FlipGFP-based executioner caspase reporter visualized apoptosis in live zebrafish embryos with spatiotemporal resolution. FlipGFP also visualized apoptotic cells in the midgut of Drosophila. Thus, the FlipGFP-based caspase reporter will be useful for monitoring apoptosis during animal development and for designing reporters of proteases beyond caspases. The design strategy can be further applied to a red fluorescent protein for engineering a red fluorogenic protease reporter.

De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles.

De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.

A naturally monomeric infrared fluorescent protein for protein labeling in vivo.

Infrared fluorescent proteins (IFPs) provide an additional color to GFP and its homologs in protein labeling. Drawing on structural analysis of the dimer interface, we identified a bacteriophytochrome in the sequence database that is monomeric in truncated form and engineered it into a naturally monomeric IFP (mIFP). We demonstrate that mIFP correctly labels proteins in live cells, Drosophila and zebrafish. It should be useful in molecular, cell and developmental biology.

Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster.

De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.

Protective effect of metformin on renal injury of C57BL/6J mouse treated with high fat diet.

This study aimed to investigate the protective effect of metformin on renal injury of C57BL/6J mice treated with a high fat diet. High-fat diet for 12 weeks was used to establish the mice model of metabolism syndrome and the intervention of metformin (75 mg x kg(-1) x d(-1)) for 4 weeks, and plasma biochemical indicator and body weight were used to evaluate the model. Sterol regulatory element-binding protein (SERBP)-1c, TNF-α, NADPH Oxidase (NOX)4 mRNA was determined by real time-PCR. Phospho-AMP-activated protein kinase (P-AMPK)α protein was detected by western blotting. Oil Red O staining, Masson staining and HE staining were for observing renal pathological changes. At the end of 12th week, compared with mice on low fat diet (LFD), body weight (BW), the levels of fasting insulin (FINS), plasma and renal triglyceride (TG) were higher and plasma high density lipoprotein (HDL) and insulin sensitivity index (ISI) were significantly lower, but the levels of fasting blood glycemia (FBG), plasma total cholesterol (TC) and renal TC had no changes; Oil Red O staining revealed renal lipids deposition, Masson staining and HE staining revealed glomerular hypertrophy, matrix increasing, and inflammatory cells infiltration in glomerular; the expression of p-AMPKα protein decreased and the expression of SREBP-1c, TNF-α, NOX4 mRNA increased significantly in mouse treated with high fat diet (HFD). Compared with the HFD group, through metformin interventing, metabolic disorders were significantly improved, renal lipids deposition and other pathological changes were ameliorated, the expression of p-AMPKα protein increased and the expression of SREBP-1c, TNF-α, NOX4 mRNA decreased significantly. Metformin improved metabolic disorders, upregulated activity of renal AMPK, diminished the expression of renal SREBP-1c, TNF-α, NOX4 mRNA, decreased accumulation of renal lipids, and prevened renal injury.

Impacts of polypropylene microplastics on the distribution of cadmium, enzyme activities, and bacterial community in black soil at the aggregate level.

Microplastics (MPs) can co-occur widely with heavy metals in soil. This study intended to investigate the influences of the co-exposure of polyethylene MPs (0.5 %, w/w) and cadmium (Cd) in black soil on the Cd distribution, enzyme activities, and bacterial communities in both bulk soil and different sized soil aggregates (> 1, 0.50-1, 0.25-0.50, and < 0.25 mm aggregates) after a 90-day incubation. Our results showed that the existence of MPs increased the distributions of Cd in >1 mm and < 0.25 mm soil aggregates and decreased its distributions in 0.50-1 mm and 0.25-0.50 mm soil aggregates. About 12.15 %-17.65 % and 9.03 %-11.13 % of Cd were distributed in the exchangeable and oxidizable forms in bulk soil and various sized soil aggregates after the addition of MPs which were higher than those in the only Cd-treated soil (11.17 %-14.72 % and 8.66 %-10.43 %, respectively), while opposite tendency was found for Cd in the reducible form. Urease and ß-glucosidase activities in the Cd-treated soils were 1.14-1.18 and 1.07-1.31 times higher than those in the Cd-MPs treated soils. MPs disturbed soil bacterial community at phylum level and increased the bacteria richness in bulk soil. The levels of predicted functional genes which are linked to the biodegradation and metabolism of exogenous substances and soil C and N cycles were altered by the co-exposure of Cd and MPs. The findings of this study could help deepen our knowledge about the responses of soil properties, especially microbial community, to the co-occurrence of MPs and heavy metals in soil.

[Lymphatic filariasis in Hubei Province: from prevailing to elimination].

Lymphatic filariasis used to highly prevalent in 69 counties (cities) with 29 million people at the risk of infection in Hubei Province. There were 2 million people infected either by B. malayi or W. bancrofti that 1.6 million microfilaremia cases and 0.4 million chronic patients. The average rate of microfilaremia among population was 5.94%. Anopheles sinensis and Culex quinquefasciatus were the principal transmitting vectors. Since 1970s, with the strategy of taking elimination of infection source as a major focus, the average rate of the microfilaremia reduced to 0.048% with a village as the unit in 1988, and reached the standard of transmission interruption. With continuous surveillance for over a decade, the province reached the goal of filariasis elimination in 2001. This paper reviews the prevalence, control and elimination process of filariasis in Hubei Province since 1950s.

[MSCT optimal examination time for unconspicuous rib fracture].

OBJECTIVE: To explore MSCT optimal examination time for patients with unconspicuous rib fracture. METHODS: Sixty-three patients with thoracic trauma from January 2009 to June 2011 were collected. They were examined by MSCT in the first week after trauma and re-examined during eighth weeks after trauma. The number of rib which had been found fractured in the first examination was compared to that in re-examinations. RESULTS: Patients with fine rib fracture often have different diagnostic results at different examination time after trauma. There was statistical difference between the number in the first week and the third week to the fifth week. CONCLUSION: MSCT could show the pathophysiological changes of rib fracture objectively in the stage between the third week and the fifth week after trauma, which is optimal examination time for the fine rib fracture.

Primary Extra Nodal Diffuse Large B-Cell Lymphoma of the Maxillary Sinus with Symptoms of Acute Pulpitis.

Diffuse large B-cell lymphoma not otherwise specified (DLBCL-NOS) is a subtype of large B-cell non-Hodgkin lymphoma with various clinical and pathological manifestations. DLBCL-NOS which primarily arises from maxillary sinus is rare and hard to diagnose due to unique anatomy. Here, we present a case of DLBCL-NOS that developed in the left maxillary sinus of a 72-year-old male, who presented with severe toothache that resembled acute pulpitis. The lesion was diagnosed and treated based on radiographs, histological, immunohistological examinations, and PET-CT analysis. Despite its rare incidence, DLBCL-NOS should still be included in differential diagnoses to rule out malignancy in cases of endodontic disease.

Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin.

To investigate the consequences of macromolecular crowding on the behavior of a globular protein, we performed a combined experimental and computational study on the 148-residue single-domain alpha/beta protein, Desulfovibrio desulfuricans apoflavodoxin. In vitro thermal unfolding experiments, as well as assessment of native and denatured structures, were probed by using far-UV CD in the presence of various amounts of Ficoll 70, an inert spherical crowding agent. Ficoll 70 has a concentration-dependent effect on the thermal stability of apoflavodoxin (DeltaT(m) of 20 degrees C at 400 mg/ml; pH 7). As judged by CD, addition of Ficoll 70 causes an increase in the amount of secondary structure in the native-state ensemble (pH 7, 20 degrees C) but only minor effects on the denatured state. Theoretical calculations, based on an off-lattice model and hard-sphere particles, are in good agreement with the in vitro data. The simulations demonstrate that, in the presence of 25% volume occupancy of spheres, native flavodoxin is thermally stabilized, and the free energy landscape shifts to favor more compact structures in both native and denatured states. The difference contact map reveals that the native-state compaction originates in stronger interactions between the helices and the central beta-sheet, as well as by less fraying in the terminal helices. This study demonstrates that macromolecular crowding has structural effects on the folded ensemble of polypeptides.

[Start-up Characteristics of SNAD Process and Functional Abundance Succession of Volcanic Rock Biological Aerated Filter].

A SNAD(simultaneous partial nitrification,ANAMMOX,and denitrification) process initiated in a submerged biological aerated filter (SBAF) was started up by seeding nitrification sludge and an ANAMMOX filter to investigate the operating characteristics and the succession of functional bacteria. The results showed that when the autotrophic nitrogen removal and denitrification were operated stably for 67 days at an initial COD concentration of 60 mg·L-1, the maximum nitrogen removal efficiency, the COD removal rate, and the nitrogen removal rate were 92.0%, 82.9%, and 2.3 kg·(m3·d)-1, respectively. Moreover, the total nitrogen removal rate of the SNAD process in this study was 12.6% higher than that of CANON process. The results of quantitative PCR showed that the abundance of AOB slightly increased, while the abundance of ANAMMOX was one order higher than that before the start-up of SNAD. In comparison, the abundances of denitrifiers and NOB remained at a relatively low level (107 copies·g-1). Taken together, these results suggested that the SBAF process with volcanic filter was beneficial for the accumulation of ANAMMOX and AOB.

Employing a Fuzzy-Based Grey Modeling Procedure to Forecast China's Sulfur Dioxide Emissions.

Effective determination of trends in sulfur dioxide emissions facilitates national efforts to draft an appropriate policy that aims to lower sulfur dioxide emissions, which is essential for reducing atmospheric pollution. However, to reflect the current situation, a favorable emission reduction policy should be based on updated information. Various forecasting methods have been developed, but their applications are often limited by insufficient data. Grey system theory is one potential approach for analyzing small data sets. In this study, an improved modeling procedure based on the grey system theory and the mega-trend-diffusion technique is proposed to forecast sulfur dioxide emissions in China. Compared with the results obtained by the support vector regression and the radial basis function network, the experimental results indicate that the proposed procedure can effectively handle forecasting problems involving small data sets. In addition, the forecast predicts a steady decline in China's sulfur dioxide emissions. These findings can be used by the Chinese government to determine whether its current policy to reduce sulfur dioxide emissions is appropriate.

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.

Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.

Protein-directed self-assembly of a fullerene crystal.

Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.

Design and characterization of swapped-domain constructs of HIV-1 glycoprotein-41 as receptors for drug discovery.

Four new swapped-domain constructs of the ectodomain of human immunodeficiency virus type 1 glycoprotein-41 (gp41) were prepared. The gp41 ectodomain consists of 50-residue N-heptad repeat (NHR), 36-residue disulfide-bonded loop and 39-residue C-heptad repeat (CHR). It folds into a hairpin structure that forms a trimer along the NHR axis. The swapped-domain proteins feature CHR domains of length 39, 28 or 21 residues preceding a 4-residue loop and a 49- or 50-residue NHR domain. The effect of CHR truncation was to expose increasing lengths of the NHR groove, including the conserved hydrophobic pocket, an important drug target. A novel method for preparing proteins with extended exposed hydrophobic surfaces was demonstrated. Biophysical measurements, including analytical ultracentrifugation and ligand-detected Water-Ligand Observed via Gradient Spectroscopy and (1)H-(15)N-HSQC NMR experiments, were used to confirm that the proteins formed stable trimers in solution with exposed binding surfaces. These proteins could play an important role as receptors in structure-based drug discovery.

The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure.