The influence of X-rays on the structural studies of peroxide-derived myoglobin intermediates

In recent years, the awareness of potential radiation damage of metal centers in protein crystals during crystallographic data collection has received increasing attention. The radiation damage can lead to radiation-induced changes and reduction of the metal sites. One of the research fields where these concerns have been comprehensively addressed is the study of the reaction intermediates of the heme peroxidase and oxygenase reaction cycles. For both the resting states and the high-valent intermediates, the X-rays used in the structure determination have given undesired side effects through radiation-induced changes to the trapped intermediates. However, X-rays have been used to generate and trap the peroxy/hydroperoxy state in crystals. In this review, the structural work and the influence of X-rays on these intermediates in myoglobin are summarized and viewed in light of analogous studies on similar intermediates in peroxidases and oxygenases.     

Synthesis, crystal structure, and DNA-cleaving behavior of 5-substituted benzene-1,3-bis(methylene)-spaced dinuclear copper(II) complexes

Three meta-dicopper complexes, 1-3, based on 5-substituted 1,3-xylylene spacer have been synthesized. These complexes are capable of inducing the transformation of supercoiled DNA (pUC19) to its nicked and linear DNA form in the presence of ascorbate, and their DNA nicking efficiency can be correlated to their DNA-binding ability. The cleavage mechanism is similar to that of the non-substituted meta-dicopper complex A. Amongst the three complexes, 5-(aminomethyl)-substituted complex 3 displayed a higher DNA-binding ability and nicking efficiency than unsubstituted complex A. The CD-spectroscopic study and structural analysis imply that the different CuCu distances and DNA binding modes induced by different 5-substituents on benzene-1,3-bis(methylene) spacer may be responsible for the different DNA cleaving behavior of meta-dicopper complexes.     

Secondary metabolites from two species of Pulicaria and their cytotoxic activity

Two new compounds, the sesquiterpene (1E,5E)-8β-acetoxy-4α-hydroxy-7βH-germacra-1(10),5-dien-14-oic acid (2), and a nor-sesquiterpene, (5E)-8β-acetoxy-4α-hydroxy-7βH-germacr-5-en-10-one (3), were isolated from Pulicaria canariensis ssp. lanata, along with ten known compounds, including the flavonoid 5,3'-dihydroxy-3,7,4'-trimethoxyflavone (4). From Pulicaria burchardii, we isolated seven known compounds; the physical and spectroscopic data of the triterpenoid 3β-hydroxytaraxaster-20-en-30-al (1) are reported. The structures of compounds 1-3 were determined on the basis of HR-MS, and 1D- and 2D-NMR studies. The structure of 2 was corroborated by X-ray crystal diffraction. Cell viability experiments revealed that the semisynthetic flavonoid 4b was the most cytotoxic compound against human leukemia cells, and the cytotoxicity was caused by induction of apoptosis, as determined by microscopy of nuclear changes.     

XANES study of the carboxylate binding mode in two pterin hydroxylases

The 2-His-1-carboxylate triad is an Fe(II)-binding motif common to several enzyme families. Within the catalytic cycle, the metal ion seems to alter between hexa- and pentacoordination, providing an open space in the Fe moiety for dioxygen binding. Anyhow, based on crystallographic studies, the picture is not fully consistent as different coordination numbers are reported for similar states. Moreover, the orientation of the metal-coordinating carboxylate varies in these studies. These differences are reflected in the XANES spectra analyzed in this paper. For isolated tyrosine and phenylalanine hydroxylase, the different active-site structures postulated by protein crystallography and further improved using spectroscopic data result in calculated XANES pattern that resemble very well the experiments. This work shows that structural differences in the non-coordinated oxygen of the carboxylate have no effect in the EXAFS but cause a change in the white-line intensity that can be successfully modeled within the muffin-tin approximation in small clusters. Thus, the study shows a way to analyze the 'carboxylate shift'. This highlights the potential of XANES analysis and clearly shows that the mentioned structural differences are present in solution as well, and does neither reflect the crystallization artifacts nor result from radiation damage or lacking resolution.     

Phytochemical Investigation and Cytotoxic Evaluation of the Components of the Medicinal Plant Ligularia atroviolacea

A phytochemical investigation of the roots of Ligularia atroviolacea resulted in the isolation of 24 compounds including seven new eremophilanoids named eremophila‐3,7(11),8‐triene‐12,8;14,6α‐diolide ( 1 ), 3β‐(angeloyloxy)eremophil‐7(11)‐en‐12,8β‐olid‐14‐oic acid ( 2 ), 1α‐chloro‐10β‐hydroxy‐6β‐(2‐methylpropanoyloxy)‐9‐oxo‐7,8‐furoeremophilane ( 3 ), (10βH)‐8‐oxoeremophila‐3(4),6(7)‐diene‐12,14‐dioic acid ( 4 ), (10αH)‐8‐oxoeremophila‐3(4),6(7)‐diene‐12,14‐dioic acid ( 5 ), 8β‐[eremophila‐3′,7′(11′)‐diene‐12′,8′α;14′,6′α‐diolide]eremophila‐3,7(11)‐diene‐12,8α;14,6α‐diolide ( 6 ), and ligulatrovine A ( 7 ), eleven known eremophilanoids, 8 – 18 , four steroids, one glucose derivative, and one fatty acid. The structures of these compounds were elucidated by spectroscopic methods including 2D‐NMR experiments. The structure of 3 was also established by an X‐ray diffraction study. The in vitro cytotoxicity evaluation of selected compounds was performed on seven cultured tumor cell lines, i.e., KB, BEL‐7404, A549, HL‐60, HeLa, CNE, and P‐388D1. The preliminary taxonomy of this species was also discussed, and the possible biogenesis of a dimer possessing a new noreremophilanoid type skeleton, 7 , is presented in a preliminary form.     

Limonoids with an Oxygen Bridge between C(1) and C(29) from the Seeds of a Krishna Mangrove,Xylocarpus granatum

Ten limonoids, named granatumins L–U ( 1 – 10 , resp.), were isolated from the seeds of an Indian mangrove, Xylocarpus granatum, collected in the estuary of Krishna, Andhra Pradesh. The structures of these compounds were established on the basis of spectroscopic data. The relative configuration of granatumin L ( 1 ) was confirmed by a single‐crystal X‐ray diffraction analysis. Granatumins L–T ( 1 – 9 , resp.) belong to the small group of limonoids with an oxygen bridge between C(1) and C(29), while granatumin U ( 10 ) is a 28‐Me‐oxidized mexicanolide. This is the first report of limonoids with an O‐bridge between C(1) and C(29) from the Indian X. granatum. The pronounced structural diversity of limonoids from this mangrove might originate from environmental factors.     

Inhibition of acid, alkaline, and tyrosine (PTP1B) phosphatases by novel vanadium complexes

In the course of our investigations of vanadium-containing complexes for use as insulin-enhancing agents, we have generated a series of novel vanadium coordination complexes with bidentate ligands. Specifically we have focused on two ligands: anthranilate (anc⁻), a natural metabolite of tryptophan, and imidizole-4-carboxylate (imc⁻), meant to mimic naturally occurring N-donor ligands. For each ligand, we have generated a series of complexes containing the V(III), V(IV), and V(V) oxidation states. Each complex was investigated using phosphatase inhibition studies of three different phosphatases (acid, alkaline, and tyrosine (PTP1B) phosphatase) as prima facia evidence for potential use as an insulin-enhancing agent. Using p-nitrophenyl phosphate as an artificial phosphatase substrate, the levels of inhibition were determined by measuring the absorbance of the product at 405 nm using UV/vis spectroscopy. Under our experimental conditions, for instance, V(imc)₃ appears to be as potent an inhibitor of alkaline phosphatase as sodium orthovanadate when comparing the K_cat/K_m term. VO(anc)₂ is as potent an inhibitor of acid phosphatase and tyrosine phosphatase as the Na₃VO₄. Thus, use of these complexes can increase our mechanistic understanding of the effects of vanadium in vivo.     

Total Synthesis of the Peptaibols Hypomurocin A3 and Hypomurocin A5, and Their Conformation Analysis

The total syntheses of hypomurocin A3 and hypomuricin A5 (HM A3 and HM A5, resp.) in solution phase are described. These syntheses have been successfully achieved by applying the ‘azirine/oxazolone method’ to introduce the two Aib‐Pro units into the backbone of these undecapeptaibols in one step with methyl 2,2‐dimethyl‐2H‐azirine‐3‐prolinate as the ‘Aib‐Pro synthon’. The coupling of Z‐protected (Z=(benzyloxy)carbonyl) amino acids or peptide acids with amino acid tert‐butyl esters and of peptide segments was carried out according to the TBTU (=O‐(benzotriazol‐1‐yl)‐N,N,N′,N′‐tetramethyluronium tetrafluoroborate) and HOBt (=1‐hydroxybenzotriazole) protocol. Purification by reversed‐phase HPLC gave the peptides in pure form. The products were characterized by optical rotation, NMR and IR spectroscopy, mass spectrometry, and elemental analysis. The crystal structures of HM A3 and of an octapeptide fragment of HM A5 could be obtained. An NMR analysis was also carried out with HM A3 and HM A5 to determine their conformations in solution. A global structural comparison between the three sequences of HM A1, HM A3, and HM A5 was performed, as well as the HPLC correlation of the natural HM A family and the synthetic samples.     

Oxidation of diiron and triiron sulfurdithiolato complexes: mimics for the active site of [FeFe]-hydrogenase

The oxidation of the hexacarbonyl(1,3-dithiolato-S,S')diiron complexes 4a-4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)(5)). For R=H, four oxidation products, 6a-6d, have been obtained. In the case of R=Me, three products, 7a-7c, were formed, and for R=1/2 (CH2)(5), only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X-Ray diffraction analyses were performed for 6a-6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density-functional theory (DFT) calculations.     

X-ray crystal structure and antioxidant activity of salidroside, a phenylethanoid glycoside

The X-ray single-crystal structure of natural salidroside (=2-(4-hydroxyphenyl)ethyl beta-D-glucopyranoside; 1), isolated from Cistanche deserticola, is reported for the first time, as well as its absolute configuration. The radical-scavenging activity of 1 towards the superoxide radical anion (O*2-) was determined experimentally by chemiluminescence measurements of the pyrogallol-luminol system, and compared to that of the corresponding aglycone, i.e., tyrosol (=4-(2-hydroxyethyl)phenol; 2).     

Tropane alkaloids from Erythroxylum caatingae Plowman

Three tropane alkaloids, 1-3, were isolated from Erythroxylum caatingae, i.e., 6β-benzoyloxy-3α-[(4-hydroxy-3,5-dimethoxybenzoyl)oxy]tropane (1), a new tropane alkaloid, along with the known alkaloids 3α,6β-dibenzoyloxytropane (2) and 6β-benzoyloxy-3α-[(3,4,5-trimethoxybenzoyl)oxy]tropane (catuabine B; 3). Their structures were determined by 2D- ((1) H and (13) C) NMR. By LC/ESI-MS/MS analysis of the fractions of alkaloids 1-3, it was possible to detect five more alkaloids, 4-8, two of these, 4 and 8, possibly being new natural products. X-Ray crystallography of the chloride derivate of 1, i.e., 6β-benzoyloxy-3α-(4-hydroxy-3,5-dimethoxybenzoyloxy)tropane hydrochloride (1a) confirmed the structure of 1. Cytotoxicity was tested against the cell lines HEp-2, NCI-H292, and KB for the MeOH extract and alkaloid 3, and antitumor activity was tested against Sarcoma 180 only for the MeOH extract.     

Biochemistry of selenium-derivatized naturally occurring and unnatural nucleic acids

Selenium (Se) can provide unique biochemical and biological functions, and properties to macromolecules, including protein and RNA. Although Se has not yet been found in DNA, identification of the presence of Se in natural tRNAs has led to discovery of the naturally occurring 2-selenouridine and 5-[(methylamino)methyl]-2-selenouridine (mnm(5)se(2)U). The Se-atoms at C(2) of the modified uridines are introduced by 2-selenouridine synthase via displacement of the S-atoms in the corresponding 2-thiouridine nucleotides of the tRNAs, and selenophosphate is used as the Se donor. The research indicated that mnm(5)se(2)U is located at the first or wobble position of the anticodons in several bacterial tRNAs, including tRNA(Lys), tRNA(Glu), and tRNA(Gln). The 2-seleno functionality on this modified nucleotide probably improves the translation accuracy and/or efficiency. These observations in vivo suggest that the presence of Se can provide natural RNAs with useful properties to better function and survival. To further investigate the biochemical and structural properties of Se-derivatized nucleic acids (SeNA), we have pioneered chemical and enzymatic synthesis of Se-derivatized nucleic acids, and introduced Se into both RNA and DNA at a variety of positions by atom-specific replacement of oxygen. This review outlines the recent advancements in chemical and biochemical syntheses, and studies of SeNAs, and their potential applications in structural and functional investigation of nucleic acids and their protein complexes.     

Sesquiterpenoids and diarylheptanoids from Nidus vespae and their inhibitory effects on nitric oxide production

Two coriamyrtin-type sesquiterpenes, fengfangin A (1) and tutin (2), and six diarylheptanoids, namely alnusone (3), centrolobol (4), muricarpone B (5), 1-(3,4-dihydroxyphenyl)-7-(4-hydroxyphenyl)heptan-3-one (6), (3S)-1-(3,4-dihydroxyphenyl)-7-(4-hydroxyphenyl)heptan-3-ol (7), and (3S)-1-(4-hydroxyphenyl)-7-(3,4-dihydroxyphenyl)heptan-3-ol (8), were isolated from the 95% EtOH extract of nidus vespae, the nest of Polistes species. Their structures were identified by spectroscopic methods. Compounds 1 and 8 are new products. The absolute configuration of 1 was determined by single-crystal X-ray diffraction analysis using Flack parameter. The biological tests showed that compounds 5, 6, and 8 could inhibit nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells with IC(50) values in the range of 13-17 μM, whereas the sesquiterpenes were inactive in this assay (>25 μM). In addition, the ecological significance of the presence of neurotoxic sesquiterpene lactones in nidus vespae is briefly discussed.     

Influence of (hydroxymethyl)pyridine and pyridine-carboxylic acids, in trans-position to the isopropylamine and amine ligands, on the cytotoxicity of platinum complexes

trans-Pt(II) Complexes with aliphatic amines and planar amines such as (hydroxymethyl)pyridines, and pyridine-3- and pyridine-4-carboxylic acids were synthesized and screened for their potential cytotoxic activity in different cancer cell lines used at the NCI for in vitro screens, i.e., MCF7, NCIH460, and SF268. The complexes studied were designed to differ in geometrical parameters such as the position of the phenyl-group substituents and the nature of the substituents themselves for gathering information about the structure-activity relationships in the trans-complexes. The variation of the substituents turns to be crucial for their biological activity, as both pyridine-3- and pyridine-4-carboxylic acids in trans-position to both amine and isopropylamine ligands provided complexes which displayed no specificity toward any type of cell tested, while (hydroxymethyl)pyridine in trans-position to isopropylamine ligands led to complexes that were clearly more effective against the cell lines tested.     

Novel endothall-containing platinum(IV) complexes: synthesis, characterization, and cytotoxic activity

Two platinum(IV) complexes (OC-6-33)-dichlorido(ethane-1,2-diamine)dihydroxidoplatinum(IV) and (OC-6-33)-diammine(dichlorido)dihydroxidoplatinum(IV) were carboxylated using demethylcantharidin as carboxylation agent. The complexes were characterized by elemental analysis, mass spectrometry, multinuclear (1H, 13C, 15N, and 195Pt) NMR spectroscopy, and, in case of (OC-6-33)-diamminebis(3-carboxy-7exo-oxabicyclo[2.2.1]heptane-2-carboxylato)dichloridoplatinum(IV) via X-ray diffraction. Cytotoxicity of the complexes was studied in seven human cancer cell lines representing five tumor entities, i.e., ovarian carcinoma (CH1, SK-OV-3), cervical carcinoma (HeLa), colon carcinoma (SW480, HCT-116), osteosarcoma (U-2 OS), and hepatocellular carcinoma (Hep G2) by means of the MTT (=3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium hydrobromide) assay.     

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1-EN residues--Asp145, Arg155, Ile204--that are key for DNA cleavage, and determined their crystal structures. The L1-EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1-EN, we performed molecular dynamics simulations using as model the structures of wild type EN-L1, of two betaB6-betaB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the betaB6-betaB5 loop shows an anticorrelated motion with the surface loops betaA6-betaA5 and betaB3-alphaB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped-out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model.     

Structure and vasorelaxant activity of floranol, a flavonoid isolated from the roots of Dioclea grandiflora

The structure of the prenylated flavanonol, floranol (1=(2R,3R)-3,5,7-trihydroxy-2-(2-hydroxyphenyl)-6-methoxy-8-(3-methylbut-2-enyl)-4H-1-benzopyran-4-one), isolated from the roots of Dioclea grandiflora (Fabaceae), was unambiguously determined by X-ray analysis. The compound was tested for vasorelaxant activity. In endothelium-containing aortic rings, floranol (1) induced a concentration-dependent vasodilator effect in vessels precontracted with 0.1 microM phenylephrine with an IC(50) value of 19.9+/-2.4 microM. The removal of endothelium or pretreatment of vessels with the NO-synthase inhibitor L-NAME did not change the IC(50) and E(max) values for floranol-induced vasorelaxation. We conclude that floranol (1) should be acting directly in the rat-aorta smooth muscle cells to produce its vasorelaxant effect. The structure-activity relationship was discussed in terms of the 3-D floranol structure determined by X-ray crystallography.     

Evolution and expression of class III peroxidases

Class III peroxidases are members of a large multigenic family, only detected in the plant kingdom and absent from green algae sensu stricto (chlorophyte algae or Chlorophyta). Their evolution is thought to be related to the emergence of the land plants. However class III peroxidases are present in a lower copy number in some basal Streptophytes (Charapyceae), which predate land colonization. Gene structures are variable among organisms and within species with respect to the number of introns, but their positions are highly conserved. Their high copy number, as well as their conservation could be related to plant complexity and adaptation to increasing stresses. No specific function has been assigned to respective isoforms, but in large multigenic families, particular structure-function relations can be expected. Plant peroxidase sequences contain highly conserved residues and motifs, variable domains surrounded by conserved residues and present a low identity level among their promoter regions, further suggesting the existence of sub-functionalization of the different isoforms.     

Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).     

Structural basis for the nuclease activity of a bacteriophage large terminase

The DNA‐packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X‐ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure‐based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended β‐sheet and an auxiliary β‐hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the β‐hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the β‐hairpin, altering active site access and the orientation of catalytically essential residues.