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Complex polysaccharide mixtures were analyzed directly without derivatization by capillary zone electrophoresis in strongly alkaline solutions and electrochemical detection at a Cu electrode. The positively charged surfactant cetyltrimethylammonium bromide was included in the electrophoresis medium in order to reverse the electroosmotic flow and permit elution to be in order of increasing polysaccharide size. Carbohydrate samples analyzed by this approach included linear maltoses, enzymatically hydrolyzed starch, and commercially available dextrans of up to an average molecular weight of 18,300. Detection by constant-potential oxidation at a Cu electrode was very sensitive, with detection limits for individual carbohydrates generally below the femtomole level.

An electrochemical pretreatment regime for a cylindrical carbon fibre microelectrode was optimized for the determination of aminopyrine (AM) and its metabolite 4-aminoantipyrine (AAN) by capillary electrophoresis (CE)-electrochemical detection (ED). Under optimized conditions, a response of high sensitivity and stability was obtained for AM and AAN at a detection voltage as low as 0.9 V following CE-ED, by which AM and AAN were separated satisfactorily. The calibration graph was linear over three orders of magnitude and the limits of detection for AM and AAN were in the femtomole range.

Crystals of extracellular fragment X3 of a human sperm membrane protein YWK-II/APPH have been grown at 291 K using 8% PEG 4000 as precipitant by the vapour-diffusion method. The diffraction pattern of the crystal extends to 2.9 A resolution at 100 K using Cu Kalpha radiation in-house. The crystals belong to space group P2(1), with unit-cell parameters a = 46.0, b = 43.7, c = 90.2 A, alpha = gamma = 90.0, beta = 106.6 degrees. Furthermore, a selenomethionine (SeMet) derivative of the protein was overexpressed in the same expression system and was purified in a reducing environment. The derivative crystals were obtained under similar conditions. Subsequently, a single-wavelength data set was collected to 2.38 A resolution from the derivative crystal at ESRF. The crystals belong to space group P2(1), with unit-cell parameters a = 46.2, b = 44.0, c = 88.3 A, alpha = gamma = 90.0, beta = 103.6 degrees. The presence of one molecule per asymmetric unit gives a crystal Volume per protein mass (V(M)) of 2.8 A(3) Da(-1) and a solvent content of 56.4% by Volume.

The cytochrome P450 enzyme CYP199A4, from Rhodopseudomonas palustris HaA2, can efficiently demethylate 4-methoxybenzoic acid. It is also capable of oxidising a range of other related substrates. By investigating substrates with different substituents and ring systems we have been able to show that the carboxylate group and the nature of the ring system and the substituent are all important for optimal substrate binding and activity. The structures of the veratric acid, 2-naphthoic acid and indole-6-carboxylic acid substrate-bound CYP199A4 complexes reveal the substrate binding modes and the side-chain conformational changes of the active site residues to accommodate these larger substrates. They also provide a rationale for the selectivity of product oxidation. The oxidation of alkyl substituted benzoic acids by CYP199A4 is more complex, with desaturation reactions competing with hydroxylation activity. The structure of 4-ethylbenzoic acid-bound CYP199A4 revealed that the substrate is held in a similar position to 4-methoxybenzoic acid, and that the C(β) C-H bonds of the ethyl group are closer to the heme iron than those of the C(α) (3.5 vs. 4.8 Å). This observation, when coupled to the relative energies of the reaction intermediates, indicates that the positioning of the alkyl group relative to the heme iron may be critical in determining the amount of desaturation that is observed. By mutating a single residue in the active site of CYP199A4 (Phe185) we were able to convert the enzyme into a 4-ethylbenzoic acid desaturase.

Fe/Woodceramics(Fe/WCMs) composites are prepared by dipping bamboo powder into ferric salt solution, dropping alkali, mixing with furane resin, and then having the mixture molded and finally sintered in high temperature. Microstructures of Fe/WCMs are measured by using X-ray diffraction(XRD) and scanning electron microscopy (SEM). XRD results indicate that the characteristic peaks of Fe are found. SEM photographs show that Fe crystals are distributed in the glassy carbon. The effects of concentration of ferric salt on volume shrinkage ratio and volume electrical resistivity of the composites are investigated. The results show that the volume shrinkage ratio and the volume electrical resistivity decrease with an increase in concentration of ferric salt.

Diabetes is a common comorbidity in cystic fibrosis (CF) that worsens prognosis. The lack of an animal model for CF-related diabetes (CFRD) has made it difficult to dissect how the onset of pancreatic pathology influences the emergence of CFRD. We evaluated the structure and function of the neonatal CF endocrine pancreas using a new CFTR-knockout ferret model. Although CF kits are born with only mild exocrine pancreas disease, progressive exocrine and endocrine pancreatic loss during the first months of life was associated with pancreatic inflammation, spontaneous hyperglycemia, and glucose intolerance. Interestingly, prior to major exocrine pancreas disease, CF kits demonstrated significant abnormalities in blood glucose and insulin regulation, including diminished first-phase and accentuated peak insulin secretion in response to glucose, elevated peak glucose levels following glucose challenge, and variably elevated insulin and C-peptide levels in the nonfasted state. Although there was no difference in lobular insulin and glucagon expression between genotypes at birth, significant alterations in the frequencies of small and large islets were observed. Newborn cultured CF islets demonstrated dysregulated glucose-dependent insulin secretion in comparison to controls, suggesting intrinsic abnormalities in CF islets. These findings demonstrate that early abnormalities exist in the regulation of insulin secretion by the CF endocrine pancreas.

Ionic liquid (IL) based dispersive liquid-liquid microextraction (DLLME) with back-extraction coupled with capillary electrophoresis ultraviolet detection was developed to determine four phenolic compounds (bisphenol-A, β-naphthol, α-naphthol, 2, 4-dichlorophenol) in aqueous cosmetics. The developed method was used to preconcentrate and clean up the four phenolic compounds including two steps. The analytes were transferred into room temperature ionic liquid (1-octyl-3-methylimidazolium hexafluorophosphate, [C(8) MIM][PF(6) ]) rich-phase in the first step. In the second step, the analytes were back-extracted into the alkaline aqueous phase. The effects of extraction parameters, such as type and volume of extraction solvent, type and volume of disperser, extraction and centrifugal time, sample pH, salt addition, and concentration and volume of NaOH in back-extraction were investigated. Under the optimal experimental conditions, the preconcentration factors were 60.1 for bisphenol-A, 52.7 for β-naphthol, 49.2 for α-naphthol, and 18.0 for 2, 4-dichlorophenol. The limits of detection for bisphenol-A, β-naphthol, α-naphthol and 2, 4-dichlorophenol were 5, 5, 8, and 100 ng mL(-1), respectively. Four kinds of aqueous cosmetics including toner, soften lotion, make-up remover, and perfume were analyzed and yielded recoveries ranging from 81.6% to 119.4%. The main advantages of the proposed method are quick, easy, cheap, and effective.

Novel monolithic capillary columns with embedded graphene were developed and used for polymer monolith microextraction (PMME) coupled to LC–MS analysis. The column was prepared inside fused silica capillaries (320 μm, i.d.) using thermally initiated free-radical polymerization with butyl methacrylate (BMA) as monomer, ethylene dimethacrylate (EDMA) as cross-linker, and 1,4-butanediol and 1-propanol as porogens. Graphene (GN) was incorporated into the poly(BMA–EDMA) monolith to enhance the loading capacity. The obtained GN and the poly(BMA–EDMA–GN) monolith were characterized by transmission electron microscope (TEM), atomic force microscopic (AFM) and scanning electron microscopy (SEM). The extraction performance of the monolithic column was evaluated by glucocorticoids (GCs) as the analytes. The operation parameters of PMME including desorption solvent, sample flow rate, sample volume, sample pH, and eluent flow rate were studied and optimized. When compared to the parent poly(BMA–EDMA) column and direct sample analysis, high enrichment capacity was observed in the case of GN-entrapped monolith. The GN incorporated monolithic capillary showed satisfactory reusability and stability during extraction. The limits of detection (S/N = 3) for nine GCs were in the range of 0.13–1.93 ng/mL. Relative standard deviations for the determination of the target GCs were less than 14.5%. Finally, the PMME method, based on the developed monolithic capillary as the extraction media, was successfully applied to the determination of nine GCs in cosmetics. The recoveries of GCs spiked in different matrices ranged from 83.7% to 103.8%.

The reaction is applied to a wide range of substituted indoles under moderate hydrogen pressure.

A novel modified electrode dispersed with ultrafine platinum particles on the surface of a 30-μm carbon fibre microelectrode was investigated as an amperometric detector in capillary zone electrophoresis (CEEC) for determining hydrazines. The unique characteristic of the Pt particle-modified carbon fibre microelectrode is its excellent stability. Hydrazines were separated and detected by CEEC with the modified microelectrode with detection limits down to the femtomole level.

MyD88 adaptor-like protein (Mal) is a crucial adaptor that acts as a bridge to recruit the MyD88 molecule to activated TLR4 receptors in response to invading pathogens. The specific assembly of the Toll/interleukin-1 receptor (TIR) domains of TLR4, Mal and MyD88 is responsible for proper signal transduction in the TLR4 signaling pathway. However, the molecular mechanism for the specificity of these TIR domains remains unclear. Here, we present the crystal structure of the TIR domain of the human Mal molecule (Mal-TIR) at a resolution of 2.4 A. Unexpectedly, Mal-TIR exhibits an extraordinarily long AB loop, but no αB helix or BB loop, distinguishing it from other TIR domains. More importantly, the Mal-TIR AB loop is capable of mediating direct binding to the TIR domains of TLR4 and MyD88 simultaneously. We also found that Mal-TIR can form a back-to-back dimer that may resemble the dimeric assembly of the entire Mal molecule. Our data demonstrate the bridge role of the Mal-TIR domain and provide important information about TIR domain specificity.

Displacement measurement by dual wavelength and single grating integrates the single grating diffraction theory and the heterodyne interference theory. By taking advantage of the two theories, it solves the contradiction between large range and high precision in grating displacement measurement quite well. In order to obtain nanometer resolution and nanometer precision, high-power subdivision of interference fringe must be realized accurately. According to phase demodulation theory for heterodyne interference signal, a digital phase measuring method is proposed by combining frequency-mixing technique and pulse-filling method. The whole signal processing part, which is based on FPGA and PLL, has been designed to realize the integer period measurement and high-powered subdivision of the decimal phase. Through experiments, it is validated that the phase range is [-180°, 180°], and the phase measurement resolution and the phase precision are above 0.03° and 0.1°, respectively. Moreover, the displacement measurement resolution and the displacement precision, corresponding to the phase indexes, are 0.167nm and 0.556nm, respectively.

The practical application of electrochemical detection in capillary electrophoresis has been hampered by irreproducibility and inconvenience related to capillary/electrode alignment. In order to eliminate these problems, a simple, flexible method by which the capillary and the working electrode were integrated into a single operational unit was devised and evaluated. The electrodes were formed by sputtering a thin conductive layer of Au or Pt onto the exit tip of the capillary. Depending on the size of the capillary used (i.e., both inner and outer diameters), Au on-capillary electrodes (OCEs) gave detection limits at the micromolar level and slightly below for the test analytes dopamine and catechol. More important, operation of the OCEs required no alignment procedures beyond immersion in the CE buffer reservoir/detector cell. OCEs used in this manner exhibited relative standard deviations of 2-4% for repeated injections even if removed from solution between runs. Finally, the Au and Pt OCEs could themselves be modified further by conventional electrochemical procedures. Here, Cu OCEs, formed by electrodeposition onto Au, were used to detect carbohydrate compounds; and an enzyme OCE, formed by adsorption of glucose oxidase onto Pt, was used to detect glucose.

A palladium particle-modified carbon fiber microdisk array electrode was designed and employed in capillary electrophoresis for the simultaneous detection of hydrazine, methylhydrazine, and isoniazid. The Pd-modified microdisk electrode had high catalytic ability for hydrazines and exhibited good reproducibility and stability. The response for hydrazine was linear over 3 orders of magnitude with a correlation coefficient of 0.993. The detection limits for hydrazine, methylhydrazine, and isoniazid were 1.2, 2.1, and 6.2 pg, respectively.

The substrate-free crystal structure of a five-mutation directed evolution variant of CYP102A1 (P450(BM3)) with generic activity-enhancing properties ("KT2") has been determined to 1.9-Å resolution. There is a close resemblance to substrate-bound structures of the wild-type enzyme (WT). The disruption of two salt bridges that link the G- and I-helices in WT causes conformational changes that break several hydrogen bonds and reduce the angle of the kink in the I-helix where dioxygen activation is thought to take place. The side-chain of a key active site residue, Phe87, is rotated in one molecule of the asymmetric unit, and the side-chains of Phe158 and Phe261 cascade into the orientations found in fatty-acid-bound forms of the enzyme. The iron is out of the porphyrin plane, towards the proximal cysteine. Unusually, the axial water ligand to the haem iron is not hydrogen-bonded to Ala264. The first electron transfer from the reductase domain to the haem domain of substrate-free KT2 is almost as fast as in palmitate-bound WT even though the reduction potential of the haem domain is only slightly more oxidising than that of substrate-free WT. However, NADPH is turned over slowly in the absence of substrate, so the catalytic cycle is gated by a step subsequent to the first electron transfer-a contrast to WT. Propylbenzene binding slightly raises the first electron transfer rate in WT but not in KT2. It is proposed that the generic rate accelerating properties of KT2 arise from the substrate-free form being in a catalytically ready conformation, such that substrate-induced changes to the structure play a less significant role in promoting the first electron transfer than in WT.

Thyroid hormone responsive protein (Thrsp, also known as Spot 14 and S14) is a carbohydrate-inducible and thyroid-hormone-inducible nuclear protein specific to liver, adipose and lactating mammary tissues. Thrsp functions to activate genes encoding fatty-acid synthesis enzymes. Recent studies have shown that in some cancers human Thrsp (hS14) localizes to the nucleus and is amplified, suggesting that it plays a role in the regulation of lipogenic enzymes during tumourigenesis. Thrsp, a member of the Spot 14 superfamily, is an acidic homodimeric protein with no sequence similarity to other mammalian gene products and its biochemical function is elusive. To shed light on the structure-function relationship of this protein, human Thrsp was crystallized. Recombinant human Thrsp (hThrsp), the N-terminally truncated human Thrsp(10-146) (hThrsp9) and their selenomethionyl (SeMet) derivatives were expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. Diffraction-quality crystals were grown at 293 K using Li(2)SO(4) as a precipitant. Using synchrotron radiation, data for the hThrsp SeMet derivative, hThrsp9 and its SeMet derivative were collected to 4.0, 3.0 and 3.6 Å resolution, respectively, at 100 K. The crystals of full-length hThrsp and its SeMet derivative belonged to space group P4(1)2(1)2, with approximate unit-cell parameters a = b = 123.9, c = 242.1 Å, α = β = γ = 90.0°. In contrast, the crystals of the truncated hThrsp9 and its SeMet derivative belonged to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 91.6, b = 100.8, c = 193.7 Å, α = β = γ = 90.0°. A molecular-replacement solution calculated using a murine Spot 14 structure as a search model indicated the presence of six molecules per asymmetric unit, comprising three hThrsp homodimers.

Cytochrome P450 (CYP) enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. In common with other members of the CYP153 family of alkane hydroxylases, CYP153C1 from the oligotrophic bacterium Novosphingobium aromaticivorans DSM 12444 can bind linear alkanes such as heptane, octane and nonane. Here, the production, purification and crystallization of CYP153C1 and the collection of high-resolution diffraction data to 1.77 Å resolution are reported. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 61.0, b = 96.3, c = 149.8 Å, α = β = γ = 90.0°. Preliminary X-ray diffraction data analysis revealed that the asymmetric unit is most likely to contain two protein molecules.

In this study, a novel method for the determination of nitroanilines in hair dye samples has been developed based on poly(methacrylic acid-co-ethylene glycol dimethacrylate) monolith microextraction (PMME) and high-performance liquid chromatography (HPLC) analysis. Four nitroanilines, p-nitroaniline (PNAL), m-nitroaniline (MNAL), o-nitroaniline (ONAL), and 2,4-dinitroaniline (DNAL), are studied as representatives. To obtain optimum extraction efficiency, several experimental parameters including sample flow rate, sample volume, sample pH, and eluent flow rate have been investigated. Under the optimal experimental conditions, the linear regression coefficients of the standard curves are greater than 0.9990. The limits of detection for p-nitroaniline, m-nitroaniline, o-nitroaniline, and 2,4-dinitroaniline are 0.012, 0.008, 0.018, and 0.005 μg/mL, respectively. The intraday and interday relative standard deviations are less than 3.1 and 5.4%, respectively. The proposed method is simple, rapid, sensitive, and competent when used for the determination of nitroanilines in hair dye samples and the accuracy is assessed through recovery experiments.

The cytochrome P450 CYP101D2 from Novosphingobium aromaticivorans DSM12444 is closely related to CYP101D1 from the same bacterium and to P450cam (CYP101A1) from Pseudomonas putida. All three are capable of oxidizing camphor stereoselectively to 5-exo-hydroxycamphor. The crystal structure of CYP101D2 revealed that the likely ferredoxin-binding site on the proximal face is largely positively charged, similar to that of CYP101D1. However, both the native and camphor-soaked forms of CYP101D2 had open conformations with an access channel. In the active site of the camphor-soaked form, the camphor carbonyl interacted with the haem-iron-bound water. Two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure: one located in the access channel, flanked by the B/C and F/G loops and the I helix, and the other in a cavity on the surface of the enzyme near the F helix side of the F/G loop. The observed open structures may be conformers of the CYP101D2 enzyme that enable the substrate to enter the buried active site via a conformational selection mechanism. The second and third binding sites may be intermediate locations of substrate entry and translocation into the active site, and provide insight into a multi-step substrate-binding mechanism.

The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.

Sometimes crystals cannot diffract X-rays beyond 3.0 Å resolution due to the intrinsic flexibility associated with the protein. Low resolution diffraction data not only pose a challenge to structure determination, but also hamper interpretation of mechanistic details. Crystals of a 25.6 kDa non-Pfam, hypothetical protein, PF2046, diffracted X-rays to 3.38 Å resolution. A combination of Se-Met derived heavy atom positions with multiple cycles of B-factor sharpening, multi-crystal averaging, restrained refinement followed by manual inspection of electron density and model building resulted in a final model with a R value of 23.5 (R(free)= 24.7). The asymmetric unit was large and consisted of six molecules arranged as a homodimer of trimers. Analysis of the structure revealed the presence of a RNA binding domain suggesting a role for PF2046 in the processing of nucleic acids.

Cystic fibrosis (CF) is a recessive disease that affects multiple organs. It is caused by mutations in CFTR. Animal modeling of this disease has been challenging, with species- and strain-specific differences in organ biology and CFTR function influencing the emergence of disease pathology. Here, we report the phenotype of a CFTR-knockout ferret model of CF. Neonatal CFTR-knockout ferrets demonstrated many of the characteristics of human CF disease, including defective airway chloride transport and submucosal gland fluid secretion; variably penetrant meconium ileus (MI); pancreatic, liver, and vas deferens disease; and a predisposition to lung infection in the early postnatal period. Severe malabsorption by the gastrointestinal (GI) tract was the primary cause of death in CFTR-knockout kits that escaped MI. Elevated liver function tests in CFTR-knockout kits were corrected by oral administration of ursodeoxycholic acid, and the addition of an oral proton-pump inhibitor improved weight gain and survival. To overcome the limitations imposed by the severe intestinal phenotype, we cloned 4 gut-corrected transgenic CFTR-knockout kits that expressed ferret CFTR specifically in the intestine. One clone passed feces normally and demonstrated no detectable ferret CFTR expression in the lung or liver. The animals described in this study are likely to be useful tools for dissecting CF disease pathogenesis and developing treatments.

The conserved DPY-30 is an essential component of the dosage compensation complex that balances the X-linked gene expression by regulation of the complex formation in Caenorhabditis elegans . The human DPY-30-like protein (DPY-30L) homolog is a conserved member of certain histone methyltransferase (HMT) complexes. In the human MLL1 (mixed-lineage leukemia-1) HMT complex, DPY-30L binds to the BRE2 homolog ASH2L in order to regulate histone 3–lysine 4 trimethylation. We have determined the 1.2-A crystal structure of the human DPY-30L C-terminal domain (DPY-30L C ). The DPY-30L C structure, harboring the conserved DPY-30 motif, is composed of two α-helices linked by a sharp loop and forms a typical X-type four-helix bundle required for dimer formation. DPY-30L C dimer formation is largely mediated by an extensive hydrophobic interface with some additional polar interactions. The oligomerization of DPY-30L C in solution, together with its reported binding to ASH2L, leads us to propose that the hydrophobic surface of the dimer may provide a platform for interaction with ASH2L in the MLL1 HMT complex.

X-prolyl aminopeptidases catalyze the removal of a penultimate prolyl residue from the N termini of peptides. Mammalian X-prolyl aminopeptidases are shown to be responsible for the degradation of bradykinin, a blood pressure regulator peptide, and have been linked to myocardial infarction. The x-ray crystal structure of human cytosolic X-prolyl aminopeptidase (XPN-PEP1) was solved at a resolution of 1.6 angstroms. The structure reveals a dimer with a unique three-domain organization in each subunit, rather than the two domains common to all other known structures of X-prolyl aminopeptidase and prolidases. The C-terminal catalytic domain of XPNPEP1 coordinates two metal ions and shares a similar fold with other prolyl aminopeptidases. Metal content analysis and activity assays confirm that the enzyme is double Mn(II) dependent for its activity, which contrasts with the previous notion that each XPNPEP1 subunit contains only one Mn(II) ion. Activity assays on an E41A mutant demonstrate that the acidic residue, which was considered as a stabilizing factor in the protonation of catalytic residue His498, plays only a marginal role in catalysis. Further mutagenesis reveals the significance of the N-terminal domain and dimerization for the activity of XPNPEP1, and we provide putative structural explanations for their functional roles. Structural comparisons further suggest mechanisms for substrate selectivity in different X-prolyl peptidases.

Calcyphosine is an EF-hand protein involved in both Ca 2 + -phosphatidylinositol and cyclic AMP signal cascades, as well as in other cellular functions. The crystal structure of Ca 2 + -loaded calcyphosine was determined up to 2.65 A resolution and reveals a protein containing two pairs of Ca 2 + -binding EF-hand motifs. Calcyphosine shares a highly similar overall topology with calmodulin. However, there are striking differences between EF-hand 4, both N-terminal and C-terminal regions, and interdomain linkers. The C-terminal domain of calcyphosine possesses a large hydrophobic pocket in the presence of calcium ions that might be implicated in ligand binding, while its N-terminal hydrophobic pocket is almost shielded by an additional terminal helix. Calcyphosine is largely monomeric, regardless of the presence of Ca 2 + . Differences in structure, oligomeric state in the presence and in the absence of Ca 2 + , a highly conserved sequence with low similarity to other proteins, and phylogeny define a new EF-hand-containing family of calcyphosine proteins that extends from arthropods to humans.

Coenzyme F420, a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F420-0 (F420 without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5′)guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F420-producing organisms, and weak sequence homologs are also found in non-F420-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and Pi or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F420 coenzyme. Large structural differences in the active site region of the non-F420-producing CofD homologs suggest that they catalyze a different biochemical reaction.

This is the publisher's version, also available electronically from http://www.jci.org/articles/view/34060

The AP-1 transcription factor modulates a wide range of cellular processes, including cellular proliferation, programmed cell death, and survival. JunD is a major component of the AP-1 complex following liver ischemia/reperfusion (I/R) injury; however, its precise function in this setting remains unclear. We investigated the functional significance of JunD in regulating AP-1 transcription following partial lobar I/R injury to the liver, as well as the downstream consequences for hepatocellular remodeling. Our findings demonstrate that JunD plays a protective role, reducing I/R injury to the liver by suppressing acute transcriptional activation of AP-1. In the absence of JunD, c-Jun phosphorylation and AP-1 activation in response to I/R injury were elevated, and this correlated with increased caspase activation, injury, and alterations in hepatocyte proliferation. The expression of dominant negative JNK1 inhibited c-Jun phosphorylation, AP-1 activation, and hepatic injury following I/R in JunD–/– mice but, paradoxically, led to an enhancement of AP-1 activation and liver injury in JunD+/– littermates. Enhanced JunD/JNK1-dependent liver injury correlated with the acute induction of diphenylene iodonium-sensitive NADPH-dependent superoxide production by the liver following I/R. In this context, dominant negative JNK1 expression elevated both Nox2 and Nox4 mRNA levels in the liver in a JunD-dependent manner. These findings suggest that JunD counterbalances JNK1 activation and the downstream redox-dependent hepatic injury that results from I/R, and may do so by regulating NADPH oxidases.

Rac-dependent NADPH oxidases generate reactive oxygen species used in cell signaling and microbial killing or both. Whereas the mechanisms leading to NADPH oxidase activation are fairly well studied, the mechanisms that control downregulation of this enzyme complex remain unclear. We hypothesized that reactive oxygen species produced by NADPH oxidase may autoregulate the complex by inhibiting Rac activity. To this end, we searched for binding partners of Rac1 and identified a tyrosine-phosphorylated fragment of MKK6 that bound to Rac1 under redox-stress conditions. Constitutively active MKK6 interacted directly with Rac1 in vitro, and this interaction was enhanced when MKK6 was phosphorylated on tyrosine 219. Both Rac1 and Rac2 immunoprecipitated an MKK6 fragment under conditions that elevate cellular peroxide levels in 293 and RAW cells, respectively. Constitutively active and wild-type MKK6 enhanced Rac-GTPase activity in vitro, and their overexpression inhibited PMA-induced NADPH oxidase activation in RAW cells. In contrast, a Y219F mutant of MKK6 only partially enhanced Rac1 GTPase activity, and its overexpression did not alter PMA-induced NADPH oxidase activation in RAW cells. Last, MKK6 deficiency led to an increase in Rac1-GTP levels in brain tissue. Our findings suggest that MKK6 downregulates NADPH oxidase activity by enhancing Rac-GTPase activity.

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF_0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP_1951), and a 12-stranded beta-barrel with a novel fold (V. parahaemolyticus VPA1032).

The strict anaerobic, thermophi- lic bacterium Moorella thermoacetica metabolizes C1 compounds for example CO2/H2, CO, formate, and methanol into acetate via the Wood/Ljungdahl pathway. Some of the key steps in this pathway include the metabolism of the C1 compounds into the methyl group of methylenetetrahydrofolate (MTHF) and the transfer of the methyl group from MTHF to the methyl group of acetyl-CoA catalyzed by methyltransferase, corrinoid protein and CO dehydrogenase/acetyl CoA synthase. Recently, we reported the crystallization of a 25 kDa methanol- induced corrinoid protein from M. thermoacetica (Zhou et al., Acta Crystallogr F 2005; 61:537-540). In this study we analyzed the crystal structure of the 25 kDa protein and provide genetic and bio- chemical evidences supporting its role in the methanol metabolism of M. thermoacetia. The 25 kDa protein was encoded by orf1948 of contig 303 in the M. thermoacetica genome. It resembles similarity to MtaC the corrinoid protein of the methanol:CoM methyltransferase system of meth- ane producing archaea. The latter enzyme system also contains two additional enzymes MtaA and MtaB. Homologs of MtaA and MtaB were found to be encoded by orf2632 of contig 303 and orf1949 of contig 309, respectively, in the M. thermoacetica genome. The orf1948 and orf1949 were co-tran- scribed from a single polycistronic operon. Metal analysis and spectroscopic data confirmed the presence of cobalt and the corrinoid in the puri- fied 25 kDa protein. High resolution X-ray crystal structure of the purified 25 kDa protein revealed corrinoid as methylcobalamin with the imidazole of histidine as the a-axial ligand replacing benzii- midazole, suggesting base-off configuration for the corrinoid. Methanol significantly activated the expression of the 25 kDa protein. Cyanide and nitrate inhibited methanol metabolism and sup- pressed the level of the 25 kDa protein. The results suggest a role of the 25 kDa protein in the methanol metabolism of M. thermoacetica. Proteins 2007;67:167-176. V C 2007 Wiley-Liss, Inc.

A corrinoid protein was induced and overexpressed in methanol-grown cells of the thermophilic anaerobic bacterium Moorella thermoacetica. The protein was purified from cytosolic extracts. After screening for crystallization conditions and optimization, crystals were obtained that diffracted strongly on a rotating-anode X-ray source. A diffraction data set was collected and processed including reflections to 1.9 A resolution. Reflections were indexed in a primitive orthorhombic cell with unit-cell parameters a = 55.69, b = 62.74, c = 34.54 A. N-­terminal amino-acid sequencing indicates that the crystals contain a C-­terminal fragment of the protein.

Regulated expression of lymphoid enhancer factor 1 (Lef-1) plays an obligatory role in the transcriptional control of epithelial bud formation during airway submucosal gland and mammary gland development. However, regions of the Lef-1 promoter required for spatial and temporal regulation during glandular development have yet to be defined. We hypothesized that a previously reported 110-bp Wnt-responsive element (WRE) in the Lef-1 promoter, which can be induced by Wnt-3a/β-catenin signals, may also play a role in regulating Lef-1 expression during airway and mammary gland development. Here we show that the Lef-1 promoter is also responsive to Wnt-1 signals in both airway and mammary epithelial cell lines. To better understand the importance of the WRE in dynamically regulating Lef-1 promoter activation in these two types of epithelia in vivo, we utilized LacZ reporter transgenic mice to evaluate the significance of Wnt-responsive sequences in the Lef-1 promoter during glandular bud formation. A 2.5-kb Lef-1 promoter fragment partially reproduced endogenous Lef-1 expression patterns in a subset of cell types involved in both mammary gland and submucosal glandular bud development. Interestingly, removal of the 110-bp WRE from the Lef-1 promoter ablated expression in nasal and tracheal submucosal glandular buds while having no significant effect on developmental expression in mammary glandular buds. These findings suggest that Wnt regulation of the Lef-1 promoter at the WRE may play an important role during airway submucosal glandular bud formation.

Inorganic pyrophosphatase (PPase; EC 3.6.1.1) from the hyperthermophile Pyrococcus horikoshii was crystallized by the hanging-drop vapour-diffusion method at pH 5.0 using polyethyleneglycol 4000 as the precipitant. The crystal belongs to space group P2(1)2(1)2, with unit-cell parameters a = 71.7, b = 86.5, c = 92.5 A, alpha = beta = gamma = 90 degrees. There are two molecules in the asymmetric unit. The crystals were stable during exposure to X-rays and a full set of X-ray diffraction data was collected to 2.7 A resolution in-house.

Planar electromagnetic sensor arrays have advantages such as nice coherence, fast response speed and high sensitivity, which can be used for micro damage inspection of crucial parts in equipment, and the key point in improving the inspection performance is to achieve a precise measurement of multi-channel transimpedances (the inductive voltages divided by the exciting current of the sensor). The principle and characteristics of planar electromagnetic sensor arrays are introduced in this paper, and a digital lock-in impedance measurement algorithm was investigated, with which the interference and noise in inductive voltage signals can be restrained effectively and the amplitude and phase of the transimpedance can be obtained with good repeatability. An eight channel impedance measurement system was established based on a field programmable gate array and utilized to inspect the micro damage in metal materials, and the experimental data were analyzed. The experimental results show that the impedance measurement has excellent repeatability when the sensor array is placed in air, and the maximum measurement error of the complete transimpedance measurement system is lower than 10%. A micro crack with a size of 1 mm (length) × 0.1 mm (width) × 1 mm (depth) can be detected through the measurement of multi-channel transimpedance in the planar electromagnetic sensor array.

IkappaB proteins play an important role in regulating NF-kappaB induction following a diverse range of environmental injuries. Studies evaluating IkappaBbeta knock-in mice (AKBI), in which the IkappaBalpha gene is replaced by the IkappaBbeta cDNA, have uncovered divergent properties of IkappaBalpha and IkappaBbeta that influence their ability to activate hepatic NF-kappaB and subsequent downstream proinflammatory processes in a stimulus-specific manner. While AKBI mice demonstrated identical levels of hepatic NF-kappaB activation in response to endotoxin, a significantly reduced level of hepatic NF-kappaB activation was observed in AKBI mice after liver ischemia/reperfusion (I/R) injury. This reduced level of NF-kappaB activation in AKBI mice after liver I/R also correlated with decreased induction of serum TNF-alpha, reduced hepatic inflammation, and increased survival. In contrast, no differences in any of these indicators were observed between AKBI mice and WT littermates after a lethal injection of LPS. Molecular studies suggest that the specificity of IkappaBalpha, but not IkappaBbeta, to properly regulate NF-kappaB induction during the acute phase of I/R injury is due to injury context-specific activation of c-Src and subsequent tyrosine phosphorylation of IkappaBalpha on Tyr42. These results demonstrate that IkappaBalpha and IkappaBbeta play unique injury context-specific roles in activating NF-kappaB-mediated proinflammatory responses and suggest that strategies aimed at inhibiting IkappaBalpha gene expression may be of potential therapeutic benefit in hepatic I/R injury.

The human dok-5 PTB domain fusion protein has been overexpressed in Escherichia coli and crystallized in a form suitable for X-ray crystallographic study. Crystals were obtained by the vapour-diffusion method. The crystal has unit-cell parameters a = b = 75.9, c = 108.0 A, alpha = beta = 90, gamma = 120 degrees and belongs to space group P3(2)21. Diffraction data were collected to 2.8 A resolution in-house. Furthermore, a selenomethionine (SeMet) derivative of dok-5 PTB domain fusion protein was overexpressed using the same expression system and was purified in a reductive environment. The derivative crystals were obtained under similar conditions. Subsequently, three different wavelength data sets were collected to 2.3 A resolution from the derivative crystal at the Advanced Photon Source, Argonne National Laboratory.

Crystals of a partial extracellular fragment of a human sperm membrane protein YWK-II/APPH have been grown at 291 K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.8 A resolution at 100 K using Cu K(alpha) radiation. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 46.009, b = 67.387, c = 149.241 A, alpha = beta = gamma = 90 degrees. The presence of two molecules per asymmetric unit gives a crystal Volume per protein mass (V(M)) of 3.51 A(3) Da(-1) and a solvent content of 64.6% by Volume. A full set of X-ray diffraction data were collected to 2.8 A resolution from the native crystal.

Spliceosome-mediated RNA trans-splicing (SMaRT) was investigated as a means for functionally correcting endogenous DeltaF508 cystic fibrosis transmembrane conductance regulator (CFTR) transcripts using in vitro human cystic fibrosis (CF) polarized airway epithelia and in vivo human CF bronchial xenografts. Recombinant adenovirus (Ad.CFTR-PTM) encoding a pre-therapeutic molecule (PTM) targeted to CFTR intron 9 corrected transepithelial cyclic AMP (cAMP)-sensitive short-circuit current (Isc) in DeltaF508 homozygous epithelia to a level 16% of that observed in normal human bronchial epithelia. Molecular analyses using RT-PCR and western blotting confirmed SMaRT-mediated partial correction of endogenous DeltaF508 messenger RNA (mRNA) transcripts and protein. In an in vivo model of DeltaF508 CF airway epithelia, human CF bronchial xenografts infected with Ad.CFTR-PTM also demonstrated partial correction of CFTR-mediated Cl- permeability at a level 22% of that seen in non-CF xenografts. These results provide functional evidence for SMaRT-mediated repair of mutant endogenous CFTR mRNA in intact polarized CF airway epithelial models.

Although lymphoid enhancer binding factor-1 (Lef-1) plays an obligatory role in airway submucosal gland (SMG) development, its expression alone is not an adequate signal for initiating gland morphogenesis. Because Lef-1 forms a bipartite transcription factor with beta-catenin to mediate wnt pathway signaling, we investigated the expression of beta-catenin and associated proteins during SMG development with both in situ hybridization and immunocytochemistry. Unexpectedly, high levels of E-cadherin mRNA were expressed by cells in developing gland buds from the earliest stages through subsequent differentiation into mature glands. In contrast, a decreased level of E-cadherin immunoreactivity in stage I gland bud cells suggested that post-translational modulation of E-cadherin protein levels may play a critical role in early stages of gland morphogenesis. Adenomatous polyposis coli (APC) mRNA was expressed relatively weakly in the developing ferret trachea, but higher levels of protein staining were observed throughout the cytoplasm of gland buds and surface epithelial cells. B-Catenin mRNA was abundantly expressed throughout the tracheal epithelium and at the highest levels in primordial gland buds. B-Catenin protein localized to the basolateral membranes of all airway epithelial cell types. However, no detectable increases in nuclear or cytoplasmic staining were associated with gland buds, as would be expected if beta-catenin served as a transcriptional cofactor for Lef-1 in gland morphogenesis. Additional studies demonstrated the gamma-catenin distribution to be remarkably similar to that of beta-catenin, whereas alpha-catenin staining was more diffuse in the cytoplasm of airway epithelial and gland bud cells. These descriptive results do not rule out a role for wnt signaling in SMG development , but provide no evidence that beta-catenin, or gamma-catenin, is a cofactor in Lef-1 regulation of SMG development.

A kind of software solution is provided to implement counting and division of moire fringes in this paper. No complex electronic circuit of digital counter exists in the digital reader that adopts this software solution. The counting and division of the fringes are completed in DSP (digital signal processor), so it can solve the problems that counting circuit can't match the subdivision system properly by logical judgement. Because of utilizing high-speed optoelectronic convertor and flash sample technique, the system can process moire signal with wide frequency range. The example demonstrated in the paper can count and divide signals from DC to 1MHz, i.e., if the optical sensitivity of the signal is 1 fringe per micrometers , the fastest measure speed can reach 1000mm/s. The experimental result shows that the software solution has high accuracy and sound reliability.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Based on the math-model of coordinate measurement of the two-CCDs vision sensor, which is established in this paper, the relationships among the coordinate measuring precision, the effective viewing field, the structural parameters of this sensor and the parameters of CCD itself are analyzed. In the meantime, the optimal structure layout is performed by means of computer simulation. And the simulation results show that the optimal layout of the two-CCDs vision sensor is symmetric structure.

For many inherited and acquired hepatic diseases, liver transplantation is the only possible therapeutic strategy. Ischemia/reperfusion (I/R) damage to donor tissue is thought to be one component that may play a role in the decline of posttransplant tissue function and ultimately rejection. The transcription factors, AP-1 and nuclear factor kappaB (NF-kappaB), play important roles in the acute cellular responses to tissue damage, as well as the inflammatory phase following I/R. We have found that the DNA binding activity of AP-1 was dramatically increased following warm ischemia at 1 to 3 hours postreperfusion. Induced DNA binding activity was composed of predominately c-Jun and JunD hetero- and homodimers as determined by electrophoretic mobility supershift assays. This increase in AP-1 activity occurred in the absence of significant changes in the steady-state protein levels of c-Jun and JunB. Maximal activation of Jun amino-terminal kinase ( JNK) occurred within the 25 to 30 minutes postreperfusion, just before the peak in AP-1 DNA binding. These findings suggest that phosphorylation may play an important role in regulating AP-1 transcriptional complexes. Furthermore, JunD protein levels slightly increased at 3 hours postreperfusion, concordant with changes in AP-1 DNA binding activity. The activation of NF-kappaB at 1 hour postreperfusion was independent of proteolytic degradation of IkappaB- or IkappaB-beta. This activation of NF-kappaB DNA binding activity in the nucleus was preceded by an increase in tyrosine phosphorylation of IkappaB-. These studies suggest that JNK, IkappaB tyrosine kinase, and JunD are potential targets for therapeutic intervention during liver I/R injury.