Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction

Dihydroorotate dehydrogenase (DHOD) from Trypanosoma cruzi (TcDHOD) is a member of family 1A DHOD that catalyzes the oxidation of dihydroorotate to orotate (first half-reaction) and then the reduction of fumarate to succinate (second half-reaction) in the de novo pyrimidine biosynthesis pathway. The oxidation of dihydroorotate is coupled with the reduction of FMN, and the reduced FMN converts fumarate to succinate in the second half-reaction. TcDHOD are known to be essential for survival and growth of T. cruzi and a validated drug target. The first-half reaction mechanism of the family 1A DHOD from Lactococcus lactis has been extensively investigated on the basis of kinetic isotope effects, mutagenesis and X-ray structures determined for ligand-free form and in complex with orotate, the product of the first half-reaction. In this report, we present crystal structures of TcDHOD in the ligand-free form and in complexes with an inhibitor, physiological substrates and products of the first and second half-reactions. These ligands bind to the same active site of TcDHOD, which is consistent with the one-site ping-pong Bi-Bi mechanism demonstrated by kinetic studies for family 1A DHODs. The binding of ligands to TcDHOD does not cause any significant structural changes to TcDHOD, and both reduced and oxidized FMN cofactors are in planar conformation, which indicates that the reduction of the FMN cofactor with dihydroorotate produces anionic reduced FMN. Therefore, they should be good models for the enzymatic reaction pathway of TcDHOD, although orotate and fumarate bind to TcDHOD with the oxidized FMN and dihydroorotate with the reduced FMN in the structures determined here. Cys130, which was identified as the active site base for family 1A DHOD (Fagan, R. L., Jensen, K. F., Bjornberg, O., and Palfey, B. A. (2007) Biochemistry 46, 4028-4036.), is well located for abstracting a proton from dihydroorotate C5 and transferring it to outside water molecules. The bound fumarate is in a twisted conformation, which induces partial charge separation represented as C 2 (delta-) and C 3 (delta+). Because of this partial charge separation, the thermodynamically favorable reduction of fumarate with reduced FMN seems to proceed in the way that C 2 (delta-) accepts a proton from Cys130 and C 3 (delta+) a hydride (or a hydride equivalent) from reduced FMN N 5 in TcDHOD.     

Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase,a potential drug target

Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc₁ complex inhibitor.     

The effect of molecular packing on the occurrence of spin crossover phenomena in one-dimensional Fe(II)-bis-Schiff base complexes

Two new one-dimensional Fe(II)-bis-Schiff base complexes, [Fe(L1)(pyz)] · CH₂Cl₂ (1) and [Fe(L2)(pyz)] · 2CH₂Cl₂ (2) (H₂L1 = bis(O-vanillin)-O-phenylenediimine, H₂L2 = bis(O-vanillin)-2,3-naphthalenediimine, pyz = pyrazine) are reported with their crystal structures and magnetic property. Compound 1 shows a two-step SCO behavior while 2 shows HS at all the temperature range measured. Although the extension of aromatic moiety from benzene (L1) to naphthalene (L2) was introduced for the purpose of strengthening the cooperativity, it leads to the absence of SCO, due to the unanticipated π–π interaction, which leads to the longer Fe–N bond lengths and a weak ligand field around Fe(II) ion.     

Photosynthesis-dependent Ca2+ influx and functional diversity between phospholipases in the formation of cell polarity in migrating cells of red algae

Unicellular spore cells, designated as monospores (also called archeospores), are well known as migrating plant cells, in which establishment of the anterior-posterior axis directs asymmetrical distribution of F-actin. Since the mechanisms of cell polarity formation are not yet fully elucidated in monospores, we investigated the roles of phosphoinositide signaling systems and Ca²⁺ mobilization in migration. Although we have already found the critical involvement of phosphatidylinositol 3-kinase in the establishment of cell polarity, we recently demonstrated the important roles of extracellular Ca²⁺ influx, phospholipase C (PLC) and phospholipase D (PLD). The remarkable characteristics of these factors are that Ca²⁺ influx depends on photosynthetic activity and that PLC and PLD play roles in the establishment and maintenance of cell polarity, respectively. These findings could provide new insight into the regulation of migration in eukaryotic cells.Key words: Ca²⁺ influx, cell polarity, phospholipase C, phospholipase D, photosynthesis, Porphyra yezoensisMonospores are responsible for asexual and clonal propagation of the marine multicellular red algae Porphyra and have an exceptional characteristic as migrating plant cells.^1–5 Monospores possess a round shape just after release from gametophytic blades (Fig. 1A and B), then undergo morphological change during migration. The establishment of cell polarity leads to the determination of anterior-posterior axis and asymmetrical localization of F-actin (Fig. 1C). After migration, monospores adhere to the substratum in which the apical-basal axis has been established for further development (Fig. 1D). Asymmetrical distribution of F-actin is also found in chemotaxic migration of Dictyostelium cells and leukocytes.^6,7 In these cells, reciprocal local accumulation of phosphoinositides, such as phosphatidylinositol-3,4,5-trisphosphate [PtdIns(3,4,5)P₃] at the leading edge and phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P₂] at the trailing side, is critical for the establishment of cell polarity. Phosphatidylinositol 3-kinase (PI3K) and PtdIns(3,4,5)P₃-specific D-3-phosphatase PTEN have been identified as key modulators in the establishment of cell polarity, bringing asymmetrical distribution of these two phosphoinositides in plasma membranes.^6,8 Similarly, we found the involvement of PI3K activity in the establishment of cell polarity in migrating monospores,³ suggesting the evolutional conservation of the function of PI3K in migrating eukaryotic cells. On the other hand, the importance of cell wall synthesis has been found in the maintenance of the cell polarity during monospore migration⁴ as reported in Fucus zygotes.^9,10 Therefore, the establishment and maintenance of cell polarity are thought to be regulated separately in monospores of P. yezoensis. In this addendum, further evidence of differential regulation of cell polarity formation by extracellular Ca²⁺ influx and phospholipases in migrating monospores of red algae is documented according to our recent report.⁵Open in a separate windowFigure 1Establishment and maintenance of cell polarity in monospores from the red alga P. yezoensis. (A) Discharge of unicellular monospores from a multicellular gametophytic blade of P. yezoensis strain TU-1. Scale bar = 20 µm. (B–D) Asymmetrical distribution of F-actin during early development of monospores. F-actin was stained with alex Flour 488 phalloidin. (B) Discharged monospore. (C) Migrating monospore. (D) Adhering monospore. Upper and lower photos in each panel show bright-field and fluorescent images, respectively. Arrow in (C) indicates the direction of migration. Scale bars = 5 µm. (e) Schematic representation of our working hypothesis about the formation of cell polarity required for monospore migration. Photosynthesis-dependent [Ca²⁺]_cyt increase regulates PLC and PI3K for the establishment of cell polarity, while PLD is required for the maintenance of the established cell polarity. DG, diacylgycerol; IP3, inositol-1,4,5-trisphosphate; IP3r, IP3 receptor; PC, phosphatidylcholine.     

Ubiquitin promoter�Cterminator cassette promotes genetically stable expression of the taste-modifying protein miraculin in transgenic lettuce

Lettuce is a commercially important leafy vegetable that is cultivated worldwide, and it is also a target crop for plant factories. In this study, lettuce was selected as an alternative platform for recombinant miraculin production because of its fast growth, agronomic value, and wide availability. The taste-modifying protein miraculin is a glycoprotein extracted from the red berries of the West African native shrub Richadella dulcifica. Because of its limited natural availability, many attempts have been made to produce this protein in suitable alternative hosts. We produced transgenic lettuce with miraculin gene driven either by the ubiquitin promoter/terminator cassette from lettuce or a 35S promoter/nos terminator cassette. Miraculin gene expression and miraculin accumulation in both cassettes were compared by quantitative real-time PCR analysis, Western blotting, and enzyme-linked immunosorbent assay. The expression level of the miraculin gene and protein in transgenic lettuce was higher and more genetically stable in the ubiquitin promoter/terminator cassette than in the 35S promoter/nos terminator cassette. These results demonstrated that the ubiquitin promoter/terminator cassette is an efficient platform for the genetically stable expression of the miraculin protein in lettuce and hence this platform is of benefit for recombinant miraculin production on a commercial scale.     

Isolation of disproportionating enzyme from halotolerant microalga Dunaliella parva (Volvocales, Chlorophyceae)

Starch metabolism in Dunaliella parva Lerche is regulated by the osmolarity of the surrounding solute. Two isozymes showing amylolytic activity were obtained after purification by gel filtration chromatography. The isozymes show disproportionating activity (D‐enzyme) that is specific for malto‐oligosaccharides as substrate. Properties of the D‐enzyme in D. parva are similar to those in higher plants. The activity of the D‐enzyme is also found in various Dunaliella and Chlamydomonas, indicating that the D‐enzyme is also important in the starch metabolism in algae.     

Propioxatins A and B, new enkephalinase B inhibitors. IV. Characterization of the active site of the enzyme using synthetic propioxatin analogues

Propioxatins A and B are inhibitors of enkephalinase B, which hydrolyzes enkephalin at the Gly-Gly bond. In order to clarify the structure-activity relationships of propioxatin, several compounds were synthesized and their inhibitory activity for not only enkephalinase B but also enkephalinase A was examined. The hydroxamic acid group in propioxatin was primarily essential for coordinating the metal ion in the active site of the enzyme. Among devalyl propioxatin A derivatives, the proline-containing compounds inhibited enkephalinase B and others inhibited both enzymes. An alteration of the character of the P3' amino acid valine in propioxatin A, e.g. amidation of carboxylic acid or replacement of the side chain, caused a 2 to 400-fold decrease of the inhibitory activity for enkephalinase B or an appearance of enkephalinase A inhibition with Ki values in the micromolar range. Substitution of the proline by alanine also resulted in a 1,000-fold loss of inhibitory activity for enkephalinase B. Propioxatin A was the most potent and specific inhibitor of enkephalinase B among the synthesized compounds. These potent and specific inhibitory effects were caused by the P2' proline residue, the P3' valine side chain and its free carboxylic acid. Each of the S1', S2', and S3' subsites in an enkephalinase B active site has a large and hydrophobic pocket, but the arrangement might be unique. The results could explain why enkephalinase B does not hydrolyze longer peptides.     

Synthesis of 1-(2-Deoxy-β-D-ribofuranosyl)benzimidazole via Cyclonucleosides

Abstract

Starting from 2-chlorobenzimidazole and 1-O-acetyl-2,3,5-tri-O-benzoylribofuranose a β-D-ribonucleoside of 2-chlorobenzimidazole was obtained using Vorbrüggen's procedure. This compound was derivatized to a 2,2′-S-cyclonucleoside via 2′-O-tosylation and thiourea treatment. The cyclonucleoside was converted to 1-(2-deoxy-β-D-ribo-furanosyl) benzimidazole by Raney nickel desulfurization.