Creating Order in Ultrastable Phosphonate Metal-Organic Frameworks via Isolable Hydrogen-Bonded Intermediates.

The stability presented by trivalent metal-organic frameworks (MOFs) makes them an attractive class of materials. With phosphonate-based ligands, crystallization is a challenge, as there are significantly more binding motifs that can be adopted due to the extra oxygen tether compared to carboxylate counterparts and the self-assembly processes are less reversible. Despite this, we have reported charge-assisted hydrogen-bonded metal-organic frameworks (HMOFs) consisting of [Cr(H2O)6]3+ and phosphonate ligands, which were crystallographically characterized. We sought to use these HMOFs as a crystalline intermediate to synthesize ordered Cr(III)-phosphonate MOFs. This can be done by dehydrating the HMOF to remove the aquo ligands around the Cr(III) center, forcing metal-phosphonate coordination. Herein, a new porous HMOF, H-CALF-50, is synthesized and then dehydrated to yield the MOF CALF-50. CALF-50 is ordered, although it is not single crystalline. It does, however, have exceptional stability, maintaining crystallinity and surface area after boiling in water for 3 weeks and soaking in 14.5 M H3PO4 for 24 h and 9 M HCl for 72 h. Computational methods are used to study the HMOF to MOF transformation and give insight into the nature of the structure and the degree of heterogeneity.

Characterization and assembly of the Pseudomonas aeruginosa aspartate transcarbamoylase-pseudo dihydroorotase complex.

Pseudomonas aeruginosa is a virulent pathogen that has become more threatening with the emergence of multidrug resistance. The aspartate transcarbamoylase (ATCase) of this organism is a dodecamer comprised of six 37 kDa catalytic chains and six 45 kDa chains homologous to dihydroorotase (pDHO). The pDHO chain is inactive but is necessary for ATCase activity. A stoichiometric mixture of the subunits associates into a dodecamer with full ATCase activity. Unlike other known ATCases, the P. aeruginosa catalytic chain does not spontaneously assemble into a trimer. Chemical-crosslinking and size-exclusion chromatography showed that P. aeruginosa ATCase is monomeric which accounts for its lack of catalytic activity since the active site is a composite comprised of residues from adjacent monomers in the trimer. Circular dichroism spectroscopy indicated that the ATCase chain adopts a structure that contains secondary structure elements although neither the ATCase nor the pDHO subunits are very stable as determined by a thermal shift assay. Formation of the complex increases the melting temperature by about 30°C. The ATCase is strongly inhibited by all nucleotide di- and triphosphates and exhibits extreme cooperativity. Previous studies suggested that the regulatory site is located in an 11-residue extension of the amino end of the catalytic chain. However, deletion of the extensions did not affect catalytic activity, nucleotide inhibition or the assembly of the dodecamer. Nucleotides destabilized the dodecamer which probably accounts for the inhibition and apparent cooperativity of the substrate saturation curves. Contrary to previous interpretations, these results suggest that P. aeruginosa ATCase is not allosterically regulated by nucleotides.

The normal appearance of CT myelograms.

PURPOSE: CT myelography has been used since 1976 to diagnose neural compression in the axial skeleton. With the advent of routine MRI, its role in accurately diagnosing neural compression has been questioned as its normal appearances are not defined in the study. In this study, we examine a series of CT myelograms to define the normal appearances of the neural elements of the spine. METHODS: The CT myelograms of patients with unilateral symptoms were examined by four independent physicians. The lateral extent of contrast was examined and recorded. Concordance between the recorded extents was assessed using kappa scores. RESULTS: Thirty-six scans were reviewed. Kappa analysis shows that there is a fair agreement in the lateral extent of contrast at L1, L3 and L4. At L2 and L5, agreement is slight. CONCLUSION: The interpretation of CT myelography shows significant interobserver variability. As a result, the usefulness of this diagnostic tool can be questioned, and if misinterpreted, it could lead to questionable diagnoses and inadvertently erroneous management if used in isolation. These slides can be retrieved under Electronic Supplementary Material.

Pressure-induced activation of latent dihydroorotase from Aquifex aeolicus as revealed by high pressure protein crystallography.

Dihydroorotase (DHOase) is involved in the de novo synthesis of pyrimidine in virtually all organisms, and it is usually associated with two other enzymes found in this biosynthetic pathway, carbamylphosphate synthetase and/or aspartate transcarbamylase (ATCase). In the hyperthermophilic bacterium Aquifex aeolicus, ATCase and DHOase are noncovalently associated. Upon dissociation, ATCase keeps its activity entirely while DHOase is totally inactivated. It was previously shown that high pressure fully restores the activity of this isolated DHOase. On the basis of kinetic studies, site-directed mutagenesis and the use of peptides mimicking loop A, a loop that appears to block access to the active site, was proposed that this pressure-induced reactivation was due to the decrease in the volume of the system, -ΔV, resulting from the disruption of known ionic interactions between the loop and the main part of the protein. In this study, this interpretation is more precisely demonstrated by the determination of the crystallographic structure of isolated DHOase under pressure. In addition to the loop displacements, pressure induces a discrete rearrangement of the catalytic site aspartate 305, an effect that might additionally contribute to the reactivation of this enzyme.

Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure.

Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues.

Antimony/Graphitic Carbon Composite Anode for High-Performance Sodium-Ion Batteries.

Although the room-temperature rechargeable sodium-ion battery has emerged as an attractive alternative energy storage solution for large-scale deployment, major challenges toward practical sodium-ion battery technology remain including identification and engineering of anode materials that are both technologically feasible and economical. Herein, an antimony-based anode is developed by incorporating antimony into graphitic carbon matrices using low-cost materials and scalable processes. The composite anode exhibits excellent overall performance in terms of packing density, fast charge/discharge capability and cyclability, which is enabled by the conductive and compact graphitic network. A full cell design featuring this composite anode with a hexacyanometallate cathode achieves superior power output and low polarization, which offers the potential for realizing a high-performance, cost-effective sodium-ion battery.

The diabetic foot: the importance of coordinated care.

Because of the severe morbidity and mortality associated with diabetes, diabetic foot care is an essential component of a peripheral vascular service. The goal of this article is to describe the vascular diabetic foot care pathway and how the coordinated foot care service for diabetic patients is delivered at King's College Hospital, London.

Intersubunit communication in the dihydroorotase-aspartate transcarbamoylase complex of Aquifex aeolicus.

Aspartate transcarbamoylase and dihydroorotase, enzymes that catalyze the second and third step in de novo pyrimidine biosynthesis, are associated in dodecameric complexes in Aquifex aeolicus and many other organisms. The architecture of the dodecamer is ideally suited to channel the intermediate, carbamoyl aspartate from its site of synthesis on the ATC subunit to the active site of DHO, which catalyzes the next step in the pathway, because both reactions occur within a large, internal solvent-filled cavity. Channeling usually requires that the reactions of the enzymes are coordinated so that the rate of synthesis of the intermediate matches its rate of utilization. The linkage between the ATC and DHO subunits was demonstrated by showing that the binding of the bisubstrate analog, N-phosphonacetyl-L-aspartate to the ATC subunit inhibits the activity of the distal DHO subunit. Structural studies identified a DHO loop, loop A, interdigitating between the ATC domains that would be expected to interfere with domain closure essential for ATC catalysis. Mutation of the DHO residues in loop A that penetrate deeply between the two ATC domains inhibits the ATC activity by interfering with the normal reciprocal linkage between the two enzymes. Moreover, a synthetic peptide that mimics that part of the DHO loop that binds between the two ATC domains was found to be an allosteric or noncompletive ATC inhibitor (K(i) = 22 µM). A model is proposed suggesting that loop A is an important component of the functional linkage between the enzymes.

The mononuclear metal center of type-I dihydroorotase from Aquifex aeolicus.

BACKGROUND: Dihydroorotase (DHO) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. E. coli DHO was initially thought to have a mononuclear metal center, but the subsequent X-ray structure clearly showed two zinc ions, α and ß, at the catalytic site. Aquifex aeolicus DHO, is a dodecamer comprised of six DHO and six aspartate transcarbamoylase (ATC) subunits. The isolated DHO monomer, which lacks catalytic activity, has an intact α-site and conserved ß-site ligands, but the geometry of the second metal binding site is completely disrupted. However, the putative ß-site is restored when the complex with ATC is formed and DHO activity is regained. Nevertheless, the X-ray structure of the complex revealed a single zinc ion at the active site. The structure of DHO from the pathogenic organism, S. aureus showed that it also has a single active site metal ion. RESULTS: Zinc analysis showed that the enzyme has one zinc/DHO subunit and the addition of excess metal ion did not stimulate catalytic activity, nor alter the kinetic parameters. The metal free apoenzyme was inactive, but the full activity was restored upon the addition of one equivalent of Zn2+ or Co2+. Moreover, deletion of the ß-site by replacing the His180 and His232 with alanine had no effect on catalysis in the presence or absence of excess zinc. The 2.2 Å structure of the double mutant confirmed that the ß-site was eliminated but that the active site remained otherwise intact. CONCLUSIONS: Thus, kinetically competent A. aeolicus DHO has a mononuclear metal center. In contrast, elimination of the putative second metal binding site in amidohydrolyases with a binuclear metal center, resulted in the abolition of catalytic activity. The number of active site metal ions may be a consideration in the design of inhibitors that selectively target either the mononuclear or binuclear enzymes.

The impact of arterial pedal arch quality and angiosome revascularization on foot tissue loss healing and infrapopliteal bypass outcome.

OBJECTIVE: This study evaluated the effect of pedal arch quality on the amputation-free survival and patency rates of distal bypass grafts and its direct impact on the rate of healing and time to healing of tissue loss after direct angiosome revascularization in patients with critical limb ischemia (CLI). METHODS: Between 2004 and 2011, patients undergoing distal bypass for CLI (Rutherford 4-6) were divided in groups taking into consideration the state of the pedal arch and direct angiosome revascularization (DAR) and non-DAR. Angiography was used to divide the pedal arch into three groups: complete pedal arch (CPA), incomplete pedal arch (IPA), and no pedal arch (NPA). The primary end points were patency rates at 12 months, amputation-free survival at 48 months, and the rate of healing and time to healing of foot tissue loss. RESULTS: A total of 154 patients (75% men) with CLI underwent 167 infrapopliteal bypasses. Patients were a median age of 75 years (range, 46-96 years). Diabetic mellitus was present in 76%, chronic renal failure in 28%, and ischemic heart disease in 44%. The primary patency rates at 1 year in the CPA, IPA, and NPA groups were 58.4%, 54.6%, and 63.8%, respectively (P = .5168), the secondary patency rates were 86.0%, 84.7%, and 88.8%, respectively (P = .8940), and the amputation-free survival at 48 months was 67.2%, 69.7%, and 45.9%, respectively (P = .3883). Tissue loss was present in 141 of the 167 bypasses. In the CPA group, 83% of tissue loss with DAR healed compared with 92% in the non-DAR (median time to healing, 66 vs 74 days). Similarly in the IPA group, 90% with DAR healed compared with 81% in the non-DAR (median time to healing, 96 vs 86 days). In the NPA group, only 75% with DAR healed compared with 73% in the non-DAR (median time to healing, 90 vs 135 days). There was a significant difference in healing and time to healing between the CPA/IPA and NPA groups (P = .0264). CONCLUSIONS: The quality of the pedal arch did not influence the patency or the amputation-free survival rates. However, the rates for healing and time to healing were directly influenced by the quality of the pedal arch rather than the angiosome revascularized.

The smallest active carbamoyl phosphate synthetase was identified in the human gut archaeon Methanobrevibacter smithii.

The genome of the major intestinal archaeon Methanobrevibacter smithii contains a complex gene system coding for carbamoyl phosphate synthetase (CPSase) composed of both full-length and reduced-size synthetase subunits. These ammonia-metabolizing enzymes could play a key role in controlling ammonia assimilation in M. smithii, affecting the metabolism of gut bacterial microbiota, with an impact on host obesity. In this study, we isolated and characterized the small (41 kDa) CPSase homolog from M. smithii. The gene was cloned and overexpressed in Escherichia coli, and the recombinant enzyme was purified in one step. Chemical cross-linking and size exclusion chromatography indicated a homodimeric/tetrameric structure, in accordance with a dimer-based CPSase activity and reaction mechanism. This small enzyme, MS-s, synthesized carbamoyl phosphate from ATP, bicarbonate, and ammonia and catalyzed the same ATP-dependent partial reactions observed for full-length CPSases. Steady-state kinetics revealed a high apparent affinity for ATP and ammonia. Sequence comparisons, molecular modeling, and kinetic studies suggest that this enzyme corresponds to one of the two synthetase domains of the full-length CPSase that catalyze the ATP-dependent phosphorylations involved in the three-step synthesis of carbamoyl phosphate. This protein represents the smallest naturally occurring active CPSase characterized thus far. The small M. smithii CPSase appears to be specialized for carbamoyl phosphate metabolism in methanogens.

Development of real-time assays for impedance-based detection of microbial double-stranded DNA targets: optimization and data analysis.

A real-time, label free assay was developed for microbial detection, utilizing double-stranded DNA targets and employing the next generation of an impedimetric sensor array platform designed by Sharp Laboratories of America (SLA). Real-time curves of the impedimetric signal response were obtained at fixed frequency and voltage for target binding to oligonucleotide probes attached to the sensor array surface. Kinetic parameters of these curves were analyzed by the integrated data analysis package for signal quantification. Non-specific binding presented a major challenge for assay development, and required assay optimization. For this, differences were maximized between binding curve kinetic parameters for probes binding to complementary targets versus non-target controls. Variables manipulated for assay optimization included target concentration, hybridization temperature, buffer concentration, and the use of surfactants. Our results showed that (i) different target-probe combinations required optimization of specific sets of variables; (ii) for each assay condition, the optimum range was relatively narrow, and had to be determined empirically; and (iii) outside of the optimum range, the assay could not distinguish between specific and non-specific binding. For each target-probe combination evaluated, conditions resulting in good separation between specific and non-specific binding signals were established, generating high confidence in the SLA impedimetric dsDNA assay results.

FLASH knockdown sensitizes cells to Fas-mediated apoptosis via down-regulation of the anti-apoptotic proteins, MCL-1 and Cflip short.

FLASH (FLICE-associated huge protein or CASP8AP2) is a large multifunctional protein that is involved in many cellular processes associated with cell death and survival. It has been reported to promote apoptosis, but we show here that depletion of FLASH in HT1080 cells by siRNA interference can also accelerate the process. As shown previously, depletion of FLASH halts growth by down-regulating histone biosynthesis and arrests the cell cycle in S-phase. FLASH knockdown followed by stimulating the cells with Fas ligand or anti-Fas antibodies was found to be associated with a more rapid cleavage of PARP, accelerated activation of caspase-8 and the executioner caspase-3 and rapid progression to cellular disintegration. As is the case for most anti-apoptotic proteins, FLASH was degraded soon after the onset of apoptosis. Depletion of FLASH also resulted in the reduced intracellular levels of the anti-apoptotic proteins, MCL-1 and the short isoform of cFLIP. FLASH knockdown in HT1080 mutant cells defective in p53 did not significantly accelerate Fas mediated apoptosis indicating that the effect was dependent on functional p53. Collectively, these results suggest that under some circumstances, FLASH suppresses apoptosis.

Electronic properties of metal-arene functionalized graphene.

We have employed first-principles density-functional calculations to study the electronic characteristics of covalently functionalized graphene by metal-bis-arene chemistry. It is shown that functionalization with M-bis-arene (M = Ti, V, Cr, Mn, Fe) molecules leads to an opening in the bandgap of graphene (up to 0.81 eV for the Cr derivative), and as a result, transforms it from a semimetal to a semiconductor. The bandgap induced by attachment of a metal atom topped by a benzene ring is attributed to modification of π-conjugation and depends on the concentration of functionalizing molecules. This approach offers a means of tailoring the band structure of graphene and potentially its applications for future electronic devices.

FAM129B/MINERVA, a novel adherens junction-associated protein, suppresses apoptosis in HeLa cells.

A recent proteomics study identified FAM129B or MINERVA as a target of the MAP kinase (Erk1/2) signaling cascade in human melanoma cells. Phosphorylation of the protein was found to promote cell invasion and the dissociation of the protein from the cell-cell junctions. Suppression of apoptosis during metastasis is a prerequisite for the survival and spread of cancer cells. During apoptosis, the adherens junctions are disassembled as the dying cell retracts, and new contacts are formed between normal neighboring cells. In this study, we show that FAM129B was cytosolic in exponentially growing HeLa cells but was translocated to the adherens junctions where it colocalized with ß-catenin whenever contact between two or more cells was established. Silencing the FAM129B gene expression by specific siRNAs did not induce apoptosis or inhibit the growth of HeLa cells. However, when apoptosis was induced by exposure to TNFα/cycloheximide or other apoptotic signaling molecules, the onset of apoptosis was accelerated 3-4-fold when FAM129B was depleted. Annexin V binding, the inactivation of the DNA repair enzyme, poly(ADP-ribose) polymerase, and the activation of the caspases occurred more rapidly in the cells lacking FAM129B. The rapid induction of apoptosis in FAM129B knockdown cells was reversed by co-transfection with recombinant FAM129B, indicating that its effect on apoptosis was specific. As apoptosis proceeded, FAM129B was degraded and disappeared from the plasma membrane. Thus, one crucial facet of the mechanism by which FAM129B promotes cancer cell invasion is likely to be the suppression of apoptosis.

Efficient on-column conversion of IgG1 trisulfide linkages to native disulfides in tandem with Protein A affinity chromatography.

Protein trisulfide linkages are generated by the post-translational insertion of a sulfur atom into a disulfide bond. Molecular heterogeneity was detected in a recombinant IgG(1) monoclonal antibody (mAb) and attributed to the presence of a protein trisulfide moiety. The predominant site of trisulfide modification was the bond between the heavy and light chains. The trisulfide was eliminated during purification of the IgG(1) mAb via a cysteine wash step incorporated into Protein A affinity column chromatography. Analysis of the cysteine-treated mAb by electrophoresis and peptide mapping indicated that the trisulfide linkages were efficiently converted to intact disulfide bonds (13% trisulfide decreased consistently to 1% or less) without disulfide scrambling or an increase in free sulfhydryls. The on-column trisulfide conversion caused no change in protein folding detectable by hydrogen/deuterium exchange or differential scanning calorimetry. Consistent with this, binding of the mAb to its antigen in vitro was insensitive to the presence of the trisulfide modification and to its removal by the on-column cysteine treatment. Similar, high efficiency trisulfide conversion was achieved for a second IgG(1) mAb using the column wash strategy (at least 7% trisulfide decreased to 1% or less). Therefore, trisulfide/disulfide heterogeneity can be eliminated from IgG(1) molecules via a convenient and inexpensive procedure compatible with routine Protein A affinity capture.

Concentration of proteins and removal of solutes.

The dramatic advances in recombinant DNA and proteomics technology over the past decade have supported a tremendous growth in biologics applied to diagnostics, biomarkers, and commercial therapeutic markets. In particular, antibodies and fusion proteins have now become a main focus for a broad number of clinical indications, including neurology, oncology, and infectious diseases with projected increase in novel first-class molecules and biosimilar entities over the next several years. In line with these advances are the improved analytical, development, and small-scale preparative methods employed to elucidate biologic structure, function, and interaction. A number of established methods are used for solvent removal, including lyophilization, reverse extraction, solute precipitation, and dialysis (solvent exchange), ultrafiltration, and chromatographic techniques. Notably, advances in the miniaturization and throughput of protein analysis have been supported by the development of a plethora of microscale extraction procedures and devices that exploit a wide array of modes for small-scale sample preparation, including the concentration and desalting of protein samples prior to further analysis. Furthermore, advances in process handling and data monitoring at microscale have dramatically improved complex control and product recovery of small quantities of biologics using techniques such as lyophilization and precipitation. In contrast, the efficient concentration of feed streams during preparative chromatography has been enhanced by improvements to protein binding capacity achieved through advanced bead and ligand design. The objective of solvent removal may be to prepare or concentrate solutes for analysis, or to facilitate their production or modification. Here, we describe the most recent advances in these techniques, particularly focusing on improved capabilities for bench-scale preparative methods.

Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.

In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). In mammals the enzymes are expressed as a single polypeptide chain (CAD) in the order CPS-DHO-ATC and associate into a hexamer. This study presents the three-dimensional structure of the noncovalent hexamer of DHO and ATC from the hyperthermophile A. aeolicus at 2.3 A resolution. It is the first structure of any multienzyme complex in pyrimidine biosynthesis and is a possible model for the core of mammalian CAD. The structure has citrate, a near isosteric analogue of carbamoyl aspartate, bound to the active sites of both enzymes. Three active site loops that are intrinsically disordered in the free, inactive DHO are ordered in the complex. The reorganization also changes the peptide bond between Asp153, a ligand of the single zinc atom in DHO, and Gly154, to the rare cis conformation. In the crystal structure, six DHO and six ATC chains form a hollow dodecamer, in which the 12 active sites face an internal reaction chamber that is approximately 60 A in diameter and connected to the cytosol by narrow tunnels. The entrances and the interior of the chamber are both electropositive, which suggests that the architecture of this nanoreactor modifies the kinetics of the bisynthase, not only by steric channeling but also by preferential escape of the product, dihydroorotase, which is less negatively charged than its precursors, carbamoyl phosphate, aspartate, or carbamoyl aspartate.

Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes.

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA. The melting curve of the self-complementary single strand was also measured in solution using differential scanning calorimetry (DSC) and UV absorbance spectroscopy. Temperature dependent electronic measurements on the surface and absorbance versus temperature values measured in solution experiments were analyzed assuming a two-state process. The model analysis provided estimates of the thermodynamic transition parameters of the hairpin on the surface. Two-state analyses of optical melting data and DSC measurements provided evaluations of the thermodynamic transition parameters of the hairpin in solution. Comparison of surface and solution measurements provided quantitative evaluation of the effect of the surface on the thermodynamics of the melting transition of the DNA hairpin.