Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity

BACKGROUND

Lignin degradation leads to the formation of a broad spectrum of aromatic molecules that can be used by various fungal micro-organisms as their sole source of carbon. When grown on phenolic compounds, Penicillium simplicissimum induces the strong impression of a flavin-containing vanillyl-alcohol oxidase (VAO). The enzyme catalyses the oxidation of a vast array of substrates, ranging from aromatic amines to 4-alkyphenols. VAO is a member of a novel class of widely distributed oxidoreductases, which use flavin adenine dinucleotide (FAD) as a cofactor covalently bound to the protein. We have carried out the determination of the structure of VAO in order to shed light on the most interesting features of these novel oxidoreductases, such as the functional significance of covalent flavinylation and the mechanism of catalysis.

RESULTS

The crystal structure of VAO has been determined in the native state and in complexes with four inhibitors. The enzyme is an octamer with 42 symmetry; the inhibitors bind in a hydrophobic, elongated cavity on the si side of the flavin molecule. Three residues, Tyr108, Tyr503 and Arg504 form an anion-binding subsite, which stabilises the phenolate form of the substrate. The structure of VAO complexed with the inhibitor 4-(1-heptenyl)phenol shows that the catalytic cavity is completely filled by the inhibitor, explaining why alkylphenols bearing aliphatic substituents longer than seven carbon atoms do not bind to the enzyme.

CONCLUSIONS

The shape of the active-site cavity controls substrate specificity by providing a 'size exclusion mechanism'. Inside the cavity, the substrate aromatic ring is positioned at an angle of 18 degrees to the flavin ring. This arrangement is ideally suited for a hydride transfer reaction, which is further facilitated by substrate deprotonation. Burying the substrate beneath the protein surface is a recurrent strategy, common to many flavoenzymes that effect substrate oxidation or reduction via hydride transfer.

Towards a synthetic cell cycle

Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.

Involvement of DMT1 in uptake of Cd in MDCK cells: role of protein kinase C

The involvement of iron (Fe) transporters in the uptake of cadmium (Cd) was examined in Madin-Darby kidney cells (MDCK). The uptake of Cd displayed properties that are associated with the Fe transporter divalent metal transporter 1 (DMT1). For example, the uptake of Cd and Fe was reduced by altering the cell membrane potential. The uptake of Cd was blocked by Fe, and the uptake of Fe was blocked by Cd. Also, the uptake of Cd and Fe was higher in MDCK cells bathed in a buffer at low pH. Increased uptake of Fe and Cd was observed in the HEK-293 cell line overexpressing DMT1. Overnight treatment of MDCK cells with the protein kinase C activator phorbol 12,13-dibutyrate (PDBu) resulted in increased uptake of Cd and Fe and an increase in DMT1 mRNA. An increase in newly transcribed DMT1 mRNA was not observed, suggesting that PDBu does not increase DMT1 mRNA by activating transcription. Rather, the increase was most likely due to greater stability of DMT1 mRNA, because the rate of degradation of DMT1 mRNA was slower in MDCK cells treated with PDBu. Our results suggest that Fe and Cd are transported in MDCK cells by a transporter with biochemical properties similar to those of DMT1.

The X-ray structure of the DNA-binding domain from the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 at 2.1 A resolution

The structure of the DNA-binding domain of the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 has been solved using the multiwavelength anomalous diffraction (MAD) technique on crystals of selenomethionyl protein and refined at 2.1 A resolution. The molecule is globular, consisting of a twisted, six-stranded beta-barrel that is packed against a loose bundle of four alpha-helices. Two of the beta-strands in combination with two of the helices form a structure characteristic of the DNA-binding motif found in the CAP family of helix-turn-helix transcription factors. In Mbp1, this beta2/alpha2 motif is associated with regions of both positive electrostatic potential and sequence conservation within the Mbp1/Swi4 family, suggesting a role in DNA-binding in these proteins. A combination of structural and biochemical data further indicate a similarity to HNF3gamma/fork head, a member of the family of "winged" helix-turn-helix proteins. We propose a model for DNA-binding involving a recognition helix in the major groove, phosphodiester backbone interactions through the beta-hairpin and further base and/or phosphate interactions mediated by a C-terminal, positively charged loop.

Structure of the trigonal crystal form of bovine annexin IV

The structure of a trigonal crystal form of N-terminally truncated [des-(1-9)] bovine annexin IV, an annexin variant that exhibits the distinctive property of binding both phospholipids and carbohydrates in a Ca2+-dependent manner, has been determined at 3 A (0.3 nm) resolution -space group: R3; cell parameters: a=b=118.560 (8) A and c=82.233 (6) A-. The overall structure of annexin IV, crystallized in the absence of Ca2+ ions, is highly homologous to that of the other known members of the annexin family. The trimeric assembly in the trigonal crystals of annexin IV is quite similar to that found previously in non-isomorphous crystals of human, chicken and rat annexin V and to the subunit arrangement in half of the hexamer of hydra annexin XII. Moreover, it resembles that found in two-dimensional crystals of human annexin V bound to phospholipid monolayers. The propensity of several annexins to generate similar trimeric arrays supports the hypothesis that trimeric complexes of such annexins, including annexin IV, may represent the functional units that interact with membranes.

Structural incorporation of iron into Ge–imogolite nanotubes: a promising step for innovative nanomaterials

Iron-doped aluminogermanate nanotubes were obtained using a single step, aqueous phase synthesis protocol, resulting in a novel nanomaterial.

Interplay between microstructure and magnetism in NiO nanoparticles: breakdown of the antiferromagnetic order

The possibility of tuning the magnetic behaviour of nanostructured 3d transition metal oxides has opened up the path for extensive research activity in the nanoscale world. In this work we report on how the antiferromagnetism of a bulk material can be broken when reducing its size under a given threshold. We combined X-ray diffraction, high-resolution transmission electron microscopy, extended X-ray absorption fine structure and magnetic measurements in order to describe the influence of the microstructure and morphology on the magnetic behaviour of NiO nanoparticles (NPs) with sizes ranging from 2.5 to 9 nm. The present findings reveal that size effects induce surface spin frustration which competes with the expected antiferromagnetic (AFM) order, typical of bulk NiO, giving rise to a threshold size for the AFM phase to nucleate. Ni(2+) magnetic moments in 2.5 nm NPs seem to be in a spin glass (SG) state, whereas larger NPs are formed by an uncompensated AFM core with a net magnetic moment surrounded by a SG shell. The coupling at the core-shell interface leads to an exchange bias effect manifested at low temperature as horizontal shifts of the hysteresis loop (~1 kOe) and a coercivity enhancement (~0.2 kOe).

Maitotoxin stimulates Cd influx in Madin-Darby kidney cells by activating Ca-permeable cation channels

This study examined the role of calcium channels for the uptake of cadmium (Cd) into Madin-Darby canine kidney (MDCK) cells. Maitotoxin, an activator of different types of calcium channels, increased accumulation of 109Cd and 45Ca in MDCK cells. We found that maitotoxin increased accumulation by stimulating 109Cd influx because it did not affect efflux. An inhibitor of store-operated Ca channels, SKF96365, partially blocked 45Ca influx but did not affect 109Cd influx. Ni and Mn, and loperamide and proadifen (SKF 525a), inhibited 45Ca and 109Cd influx in cells stimulated with maitotoxin, but La and nifedipine did not. Overnight treatment with phorbol 12, 13-ibutyrate (PDBu) to activate protein kinase C resulted in a decrease in the concentration of maitotoxin needed to stimulate 45Ca and 109Cd influx. The effect of PDBu was blocked by treating cells with the protein kinase C inhibitor GF109203X. Additionally, the effect of PDBu was lost in cells treated with an inhibitor of RNA synthesis actinomycin D. These results suggest that a Ca permeable cation channel different from voltage-dependent and store-operated Ca channels mediates the uptake of Cd in MDCK cells. The expression of this channel is regulated by protein kinase C.

The role of anion exchange in the uptake of Pb by human erythrocytes and Madin-Darby canine kidney cells

Anion exchange (AE) plays a critical role in regulating intracellular pH in erythrocytes and epithelial cells and has been suggested to facilitate the transport of lead (Pb) across the erythrocyte cell membrane. In this study we examined the role of AE in the uptake of Pb by human erythrocytes and by Madin-Darby canine kidney (MDCK) cells, the kidney epithelial cell line. Functional AE in MDCK cells was evidenced by: increased uptake of SO(4)(2-) at pH 6.0 over pH 7.0, and inhibition of SO(4)(2-) uptake by the AE inhibitor 4, 4'-diisothiocyanostilbene-2, 2'- disulfonic acid (DIDS) as well as by non-halide anions. Accumulation of Pb into MDCK cells was time and temperature dependent. DIDS inhibited uptake of Pb into human erythrocytes but not MDCK cells. In conclusion, uptake of Pb into erythrocytes but not kidney epithelial cells occurs through AE.

Determination of local atomic displacements in CeO(1-x)F(x)BiS2 system

We have used Bi and Ce L3-edges extended x-ray absorption fine structure measurements to study local structure of CeO(1-x)F(x)BiS2 system as a function of F-substitution. The local structure of both BiS2 active layer and CeO1-xFx spacer layer changes systematically. The in-plane Bi-S1 distance decreases (ΔRmax ∼ 0.08 Å) and the out-of-plane Bi-S2 distance increases (ΔRmax ∼ 0.12 Å) with increasing F-content. On the other hand, the Ce-O/F distance increases (ΔRmax ∼ 0.2 Å) with a concomitant decrease of the Ce-S2 distance (ΔRmax ∼ 0.15 Å). Interestingly, the Bi-S1 distance is characterized by a large disorder that increases with F-content. The results provide useful information on the local atomic displacements in CeO(1-x)F(x)BiS2, that should be important for the understanding of the coexistence of superconductivity and low temperature ferromagnetism in this system.

Evolution of iron speciation during hydration of C4AF

It is now well accepted and demonstrated that calcium silicate, calcium aluminate and calcium sulfo aluminate (ettringite, AFm) phases exhibit a good capability to fix metals and metalloids. Unfortunately the role of minor phases and especially calcium-ferric aluminate phase, shorthand C4AF is not well defined. In other systems like in soils or sediments iron phases play a key role in the fixation of pollutant. In cement sorption isotherms, indicated that various metals can be retained by the C4AF hydrated products. Therefore the capabilities of those phase to retain heavy metal should not be neglected. Previous investigations have shown that the minerals formed during the hydration of C4AF are similar to those formed from C3A (pure tri-calcium aluminate) under comparable conditions. Nevertheless no investigation was conducted at the molecular level and there is still a controversy whether Fe substitutes for Al in the hydrated minerals in whole or in part, or if it forms FeOOH clusters scattered throughout the matrix. In this context we have conducted XAS experiments using synchrotron radiation. It was found that the hydration of C4AF forms C3AH6 (hydrogarnet) in which Fe randomly substitutes for Al as well as an amorphous FeOOH phase. Intermediate products like AFm (i.e., an ill organized lamellar phase) are also formed but rapidly evolve to C3AH6; iron does not seem to be incorporated in the AFm structure.

An x-ray absorption spectroscopy study of Ni-Mn-Ga shape memory alloys

The austenite to martensite phase transition in Ni-Mn-Ga ferromagnetic shape memory alloys was studied by extended x-ray absorption fine structure (EXAFS) and x-ray absorption near-edge structure (XANES) spectroscopy. The spectra at all the three elements', namely, Mn, Ga and Ni, K-edges in several Ni-Mn-Ga samples (with both Ni and Mn excess) were analyzed at room temperature and low temperatures. The EXAFS analysis suggested a displacement of Mn and Ga atoms in opposite direction with respect to the Ni atoms when the compound transforms from the austenite phase to the martensite phase. The first coordination distances around the Mn and Ga atoms remained undisturbed on transition, while the second and subsequent shells showed dramatic changes indicating the presence of a modulated structure. The Mn rich compounds showed the presence of antisite disorder of Mn and Ga. The XANES results showed remarkable changes in the unoccupied partial density of states corresponding to Mn and Ni, while the electronic structure of Ga remained unperturbed across the martensite transition. The post-edge features in the Mn K-edge XANES spectra changed from a double peak like structure to a flat peak like structure upon phase transition. The study establishes strong correlation between the crystal structure and the unoccupied electronic structure in these shape memory alloys.

Local structure of LiCoO2 nanoparticles studied by Co K-edge x-ray absorption spectroscopy

We have studied the local structure of LiCoO(2) nanoparticles by Co K-edge x-ray absorption spectroscopy as a function of particle size. Extended x-ray absorption fine structure data reveal substantial changes in the near neighbor distances and the associated mean square relative displacements with decreasing particle size. X-ray absorption near edge structure spectra show clear local geometrical changes with decreasing particle size, similar to those that appear in the charging (delithiation) process. The results suggest that the LiCoO(2) nanoparticles are characterized by a large atomic disorder confined to the Co-O octahedra, similar to the distortions generated during the delithiation, and this disorder should be the primary limiting factor for a reversible diffusion of Li ions when nanoparticles of LiCoO(2) are used as cathode material in rechargeable Li ion batteries.

[Prevention and treatment of secondary hyperparathyroidism in non-dialyzed patients with stage 3-5 chronic kidney diease]

Deficiencies in vitamin D and vitamin D receptor (VDR) activation adversely affect cardiovascular health in the general population and in people at high risk of cardiovascular disease, as well as contributing to secondary hyperparathyroidism in patients with chronic kidney disease (CKD). Furthermore, epidemiological and observational data indicate that there is a close interrelationship between progressive renal dysfunction in CKD, cardiovascular disease, and mortality. The causes of death in patients even with only moderate kidney dysfunction are commonly associated with cardiovascular events. Modulation of vitamin D levels results in correlative regulatory effects on mineral homeostasis, hypertension, vascular disease, and calcification, as well as a number of other endpoints in cardiac and renal disease. The use of VDR activators to treat these and other parameters outside of cardiovascular and renal disease not only results in enhanced patient health but significantly lowers the risk of mortality in CKD and non-CKD patients with low systemic activity of vitamin D. The cardiovascular and renal systems continue to demonstrate their interrelated effects on each other, particularly when vitamin D and VDR signaling are considered.

[Pathogenesis and treatment of vascular calcification in CKD]

Increased vascular calcification is a major cause of cardiovascular events in patients with chronic kidney disease (CKD). It is the result of an active ossification process counteracted by ''bone'' proteins such as osteopontin, alkaline phosphatase, osteoprotegerin, and osteocalcin. Chronic kidney disease - mineral and bone disorder (CKD-MBD) is a systemic disorder of mineral and bone metabolism that occurs in CKD. In addition to abnormalities in the serum calcium and phosphate profile, CKD-MBD is characterized by abnormalities of bone turnover, mineralization, volume and growth as well as vascular calcification. Considering that the presence and extent of vascular calcification in CKD portend a poor prognosis, many efforts have been made to shed light on this complicated phenomenon to prevent vascular calcium deposition and its progression. Indeed, careful control of calcium load, serum phosphate and parathyroid hormone along with the use of calcium-free phosphate binders and vitamin D receptor activators represent a new therapeutic armamentarium to improve quality of life and reduce mortality in CKD.

Existence of structural, electronic and magnetic correlations in Sm2NiMnO6double perovskite

Coupling between different interactions allows the control of physical aspects in multifunctional materials by perturbing any degrees of freedom. Here, we aim to probe the correlation among structural, electronic, and magnetic observables in Sm2NiMnO6(SNMO) ferromagnetic insulator double perovskite. Our employed methodology includes thermal evolution of x-ray diffraction, x-ray absorption spectroscopy, and bulk magnetometry. The magnetic ordering in SNMO adopts two transitions, atTC= 160 K due to the ferromagnetic arrangement of Ni-Mn sublattice and atTd= 34 K because of anti-parallel alignment of polarized Sm paramagnetic moments with respect to Ni-Mn network. Signature of Ni/Mn anti-site disorders are evidenced from short-range structure and magnetization analysis. The long-range as well as short-range crystal structure of SNMO undergo changes acrossTCandTd, observed through temperature dependent variation in Ni/Mn-O bonding characters. Hybridization between Ni, Mn 3d, O 2pelectronic states show changes in the vicinity of magnetic transition. The change in crystal environments governs the magnetic response by imposing alteration in metal-ligand orbital overlap. On the other hand, it is observed that application of electric bias causes monotonic reduction in the saturation magnetic moment. By using these experimental methods, we demonstrate how the structural, electronic, and magnetic properties are correlated in SNMO, which makes it a potential platform for technological usage.

Unsuccessful application of taurolidine in the treatment of fungal peritonitis in peritoneal dialysis

Fungal peritonitis (FP) is a serious complication for peritoneal dialysis (PD) patients, determining hospitalization, technique failure, catheter loss and death. In the 2005 update, treatment recommendations for FP from the International Society of Peritoneal Dialysis (ISPD) advocate catheter removal immediately after fungi are identified by microscopy or culture. The availability of more effective medical treatments could therefore be of great importance. The aim of this report is to describe a case of a 43-year-old, diabetic, HIV positive PD patient with fluconazole resistant Candida peritonitis, who was treated with an i.p. taurolidine solution. Taurolidine is a non-antibiotic antimicrobial, with broad bactericidal and fungicidal properties. It has been used during surgery for lavage of the peritoneum in cases of peritonitis. Its mechanism of action is related to direct toxic action on micro-organisms, through a chemical reaction between active taurolidine derivatives and structures on the cell wall. Treatment failed because the patient had severe burning pain during i.p. administration of the drug, limiting its dose. PD catheter removal allowed complete recovery. It remains undetermined if, with different doses and methodology, taurolidine could be more effective in treating bacterial and/or fungal peritonitis. Currently, catheter removal remains the most effective therapy of fungal peritonitis.

Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a

CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.