Biosynthesis of long-chain polyamines by crenarchaeal polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum

Polyamines are ubiquitously present in all organisms. In addition to the common polyamines, thermophilic archaea synthesize long-chain polyamines. In the present study polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum were cloned and their substrate specificity was analyzed. The polyamine synthase HbSpeE II from H. butylicus synthesized long-chain polyamines with high activity using the same mechanism that is used by a wide range of organisms to synthesize common polyamines, in which the aminopropyl residue derives from decarboxylated S-adenosylmethionine. This is the first polyamine synthase described that synthesizes a polyamine longer than a tetramine with high activity.     

Characterization of the formation of amyloid protofibrils from barstar by mapping residue-specific fluorescence dynamics

The small protein barstar aggregates at low pH to form soluble oligomers, which can be transformed into fibrillar aggregates at an elevated temperature. To characterize structurally, with residue-specific resolution, the process of amyloid formation of barstar, as well as to monitor the increase in size that accompanies the aggregation process, time-resolved fluorescence anisotropy decay measurements have been introduced as a valuable probe. Seven different single-cysteine-containing mutant forms of barstar were made, to each of which a fluorophore was attached at the thiol group. The rotational dynamics of these seven fluorophores, as well as of the sole intrinsic tryptophan residue in the protein, were determined in the amyloid protofibrils formed, as well as in the soluble oligomers from which the protofibrils arise upon heating. Mapping of the fast rotational dynamics onto the sequence of the protein yields dynamic amplitude maps that allowed identification of the segments of the chain that possess local structure in the soluble oligomer and amyloid protofibrils. The patterns of these maps of the soluble oligomer and protofibrils are seen to be similar; and protofibrils display more local structure than do the soluble oligomers, at all residue positions studied. The observation that transformation from soluble oligomers to protofibrils does not perturb local structure significantly at eight different residue positions, suggests that the soluble oligomers transform directly into protofibrils, without undergoing drastic structural rearrangements.     

Facile Post-Synthetic Derivatization of Oligodeoxynucleotide Containing 5-Methoxycarbonylmethyl-2′-Deoxyuridine

Abstract

5-Methoxycarbonylmetyl-2′-deoxyuridine residue was incorporated into oligoDNAs containing either an exclusive thymidine residue (dT) or all four natural deoxynucleoside residues (dA, dG, dC, dT) via a phosphoramidite method. The treatment of the fully protected oligomer bound to controlled pore glass (CPG), with a variety of polyamine resulted in the release of the oligomer from CPG and the incorporation of the polyamine at the 5-position of the uracil component, simultaneously and in good yields.     

O-acetylated oligosaccharides from pectins of potato tuber cell walls.

Acetylated trigalacturonides and rhamnogalacturonan I (RG-I)-derived oligosaccharides were isolated from a Driselase digest of potato tuber cell walls by ion-exchange and size-exclusion chromatography. The oligosaccharides were structurally characterized by fast atom bombardment-mass spectroscopy, nuclear magnetic resonance spectroscopy, and glycosyl-linkage composition analysis. One trigalacturonide contained a single acetyl group at O-3 of the reducing galacturonic acid residue. A second trigalacturonide contained two acetyl substituents, which were located on O-3 or O-4 of the nonreducing galacturonic acid residue and O-3 of the reducing galacturonic acid residue. RG-I backbone-derived oligomers had acetyl groups at O-2 of the galacturonic acid residues. Some of these galacturonic acid residues were O-acetylated at both O-2 and O-3 positions. Rhamnosyl residues of RG-I oligomers were not acetylated.     

Structural studies by NMR spectroscopy of the major oligomers from alkali-degraded arabinoigalactan from Larix occidentalis

Oligomers with terminal metasaccharinic acid residues have been derived from branches on the main chain of arabinogalactan by alkaline degradation. The major oligomers present have been studied by NMR. Individual oligomers existed as epimeric pairs in the approximate ratio 1.5:1. This study confirmed the presence of branches consisting of a single β- -Ga1p residue, of two or three β- -Galp residues linked (1→6) or of two β-D-Ga1p residues linked (1→6) with the proximate residue further substituted at O-3 by an α- -arabinofuranosyl residue.     

Preparation of oligodeoxyribonucleoside methylphosphonates on a polystyrene support.

An efficient procedure is described for synthesizing deoxyribonucleoside methylphosphonates on polystyrene polymer supports which involves condensing 5'-dimethoxytrityldeoxynucleoside 3'-methylphosphonates. The oligomers are removed from the support and the base protecting groups hydrolyzed by treatment with ethylenediamine in ethanol, which avoids hydrolysis of the methylphosphonate linkages. Two types of oligomers were synthesized: those containing only methylphosphonate linkages, d-Np(Np)nN, and those which terminate with a 5' nucleotide residue, dNp (Np)nN. The latter oligomers can be phosphorylated by polynucleotide kinase, and are separated by polyacrylamide gel electrophoresis according to their chain length. Piperdine randomly cleaves the oligomer methylphosphonate linkages and generates a series of shorter oligomers whose number corresponds to the length of the original oligomer. Apurinic sites introduced by acid treatment spontaneously hydrolyze to give oligomers which terminate with free 3' and 5' OH groups. These reactions may be used to characterize the oligomers.     

Characterization of oligosaccharides from industrial fermentation residues by matrix-assisted laser desorption/ionization,electro spray mass spectrometry,and gas chromatography mass spectrometry

We report here the preliminary characterization of oligosaccharides present in an enzyme-treated industrial fermentation residue using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), electrospray ion trap mass spectrometry (ESI-ITMS), and gas chromatography mass spectrometry (GC-MS). After sample cleaning with carbon graphite columns, analysis of oligosaccharides present in the sample using MALDI-TOF-MS resulted in identification of molecular ions representing sodiated hexose and pentose oligo/polysaccharides. The GC-MS analyses revealed that the signals observed in the mass spectrum for hexose oligomers represent linear structures, whereas the pentose oligomers were identified as arabinoxylans with a (1-->4) linked Xylp backbone where the Xylp residues were either not substituted or singly substituted with Araf branching residues at positions C-2 or C-3 of the Xylp ring. Analyses by ESI-ITMS of the signals corresponding to arabinoxylan oligosaccharides with four and five monosaccharide residues showed the presence of isomeric structures differing in degree of branching and localization of the branched residue along the Xylp backbone.     

Synthesis and properties of pyrrolidine-based negatively charged DNA mimics

A set of novel chiral pyrrolidine-based nucleotide mimics, in which nucleobase, hydroxyl group and phosphonic acid residue were attached to different carbon atoms of the pyrrolidine ring, was synthesized. These monomers were used for the synthesis of the corresponding oligomers, and their physico-chemical properties were evaluated.     

Silica-precipitating peptides from diatoms. The chemical structure of silaffin-A from Cylindrotheca fusiformis

Two silica-precipitating peptides, silaffin-1A(1) and-1A(2), both encoded by the sil1 gene from the diatom Cylindrotheca fusiformis, were extracted from cell walls and purified to homogeneity. The chemical structures were determined by protein chemical methods combined with mass spectrometry. Silaffin-1A(1) and -1A(2) consist of 15 and 18 amino acid residues, respectively. Each peptide contains a total of four lysine residues, which are all found to be post-translationally modified. In silaffin-1A(2) the lysine residues are clustered in two pairs in which the epsilon-amino group of the first residue is linked to a linear polyamine consisting of 5 to 11 N-methylated propylamine units, whereas the second lysine is converted to epsilon-N,N-dimethyllysine. Silaffin-1A(1) contains only a single lysine pair exhibiting the same structural features. One of the two remaining lysine residues was identified as epsilon-N,N,N-trimethyl-delta-hydroxylysine, a lysine derivative containing a quaternary ammonium group. The fourth lysine residue again is linked to a long-chain polyamine. Silaffin-1A(1) is the first peptide shown to contain epsilon-N,N,N-trimethyl-delta-hydroxylysine. In vitro, both peptides precipitate silica nanospheres within seconds when added to a monosilicic acid solution.     

Mode of action of chitin deacetylase from Mucor rouxii on N-acetylchitooligosaccharides.

The mode of action of chitin deacetylase from the fungus Mucor rouxii on N-acetylchitooligosaccharides with a degree of polymerization 1-7 has been elucidated. Identification of the sequence of chitin oligomers following enzymatic deacetylation was verified by the alternative use of two specific exo-glycosidases in conjunction with HPLC. The results were further verified by 1H-NMR spectroscopy. It was observed that the length of the oligomer is important for enzyme action. The enzyme cannot effectively deacetylate chitin oligomers with a degree of polymerization lower than three. Tetra-N-acetylchitotetraose and penta-N-acetylchitopentaose are fully deacetylated by the enzyme, while in the case of tri-N-acetylchitotriose, hexa-N-acetylchitohexaose and hepta-N-acetylchitoheptaose the reducing-end residue always remains intact. Furthermore, the enzyme initially removes an acetyl group from the nonreducing-end residue of all chitin oligomers with a degree of polymerization higher than 2, and further catalyses the hydrolysis of the following acetamido groups in a processive fashion. The results are in agreement with the mode of action that the same enzyme exhibits on partially deacetylated water soluble chitosan polymers.     

Interactions of cartilage proteoglycans with hyaluronate. Inhibition of the interaction by modified oligomers of hyaluronate.

Oligomers of hyaluronic acid were prepared by digestion of hyaluronic acid from rooster combs with testicular hyaluronidase (hyaluronate 4-glycanohydrolase, EC 3.2.1.35), leech head hyaluronidase (hyaluronate 3-glycanohydrolase, EC 3.2.1.36), and with fungal hyaluronidase (hyaluronate lyase from Streptomyces hyalurolyticus). The oligomers were fractionated by gel permeation, using Sephadex G-50. Oligomers isolated after incubation of the hyaluronic acid with the testicular hyaluronidase were further modified. To prepare oligomers with N-acetylglucosamine at both ends, terminal nonreducing glucuronic acid residues were removed with beta-glucuronidase. Reducing terminal N-acetylglucosamine residues were removed by reaction under mildly alkaline conditions. The reducing terminal N-acetylglucosamine residues were also reduced with sodium borohydride to form N-acetylglucosaminitol. The potentials of the various oligosaccharides to bind to the proteoglycan from bovine nasal septum cartilage were estimated by determining their effectiveness as inhibitors of the proteoglycan-hyaluronate interaction. The present study shows that, to bind maximally to the proteoglycan, the hyaluronate oligosaccharide must be at least 10 sugar residues in length and be terminated at the nonreducing and reducing ends with a glucuronate residue and an N-acetylglucosamine residue, respectively. Sugar residues extended beyond this basic decasaccharide, do not interact with the hyaluronate binding site on the proteoglycan.     

Antiparallel Triple-strand Architecture for Prefibrillar Aβ42 Oligomers

Aβ42 oligomers play key roles in the pathogenesis of Alzheimer disease, but their structures remain elusive partly due to their transient nature. Here, we show that Aβ42 in a fusion construct can be trapped in a stable oligomer state, which recapitulates characteristics of prefibrillar Aβ42 oligomers and enables us to establish their detailed structures. Site-directed spin labeling and electron paramagnetic resonance studies provide structural restraints in terms of side chain mobility and intermolecular distances at all 42 residue positions. Using these restraints and other biophysical data, we present a novel atomic-level oligomer model. In our model, each Aβ42 protein forms a single β-sheet with three β-strands in an antiparallel arrangement. Each β-sheet consists of four Aβ42 molecules in a head-to-tail arrangement. Four β-sheets are packed together in a face-to-back fashion. The stacking of identical segments between different β-sheets within an oligomer suggests that prefibrillar oligomers may interconvert with fibrils via strand rotation, wherein β-strands undergo an ∼90° rotation along the strand direction. This work provides insights into rational design of therapeutics targeting the process of interconversion between toxic oligomers and non-toxic fibrils.     

Morphogenic effects of ezrin require a phosphorylation-induced transition from oligomers to monomers at the plasma membrane

ERM (ezrin, radixin, moesin) proteins act as linkers between the plasma membrane and the actin cytoskeleton. An interaction between their NH(2)- and COOH-terminal domains occurs intramolecularly in closed monomers and intermolecularly in head-to-tail oligomers. In vitro, phosphorylation of a conserved threonine residue (T567 in ezrin) in the COOH-terminal domain of ERM proteins disrupts this interaction. Here, we have analyzed the role of this phosphorylation event in vivo, by deriving stable clones producing wild-type, T567A, and T567D ezrin from LLC-PK1 epithelial cells. We found that T567A ezrin was poorly associated with the cytoskeleton, but was able to form oligomers. In contrast, T567D ezrin was associated with the cytoskeleton, but its distribution was shifted from oligomers to monomers at the membrane. Moreover, production of T567D ezrin induced the formation of lamellipodia, membrane ruffles, and tufts of microvilli. Both T567A and T567D ezrin affected the development of multicellular epithelial structures. Collectively, these results suggest that phosphorylation of ERM proteins on this conserved threonine regulates the transition from membrane-bound oligomers to active monomers, which induce and are part of actin-rich membrane projections.     

Hormone-independent polyamine metabolism of squamous cell carcinoma of the prostate

The levels of polyamines and their synthesizing enzymes in squamous cell carcinoma of prostate implanted in intact as well as castrated male rats were determined after certain hormonal manipulations. The tumour was found to grow with an identical rate in non-castrated and castrated rats. Polyamine content and activities of polyamine synthesizing enzymes in the tumour were found to be much lower compared to their values in ventral prostate. Moreover, the levels of these parameters were comparable in tumours whether implanted in non-castrated or gonadectomized animals. The sequential analyses of putrescine and spermidine and activities of L-ornithine decarboxylase and S-adenosyl-L-methionine decarboxylase of tumours at different time intervals showed a significant reduction in their levels at 30 days compared to 10 days post implantation in non-castrated as well as castrated rats. Daily intramuscular administration of tumour-bearing intact or castrated animals with testosterone (50 micrograms/g), beta-estradiol (2 micrograms/g) or cyproterone (12.5 micrograms/g) for 10 days did not influence polyamine metabolism in tumour tissue. However, either beta-estradiol and cyproterone treatments or castration were found to decrease polyamine synthesis in ventral prostate. At the same time, the testosterone replacement therapy did not allow polyamine levels or activities of polyamine synthesizing enzymes to decline in the ventral prostate of castrated rats. Our results demonstrated that contrary to ventral prostate, the polyamine metabolism in squamous cell carcinoma of prostate is independent of hormonal control. The loss of hormonal sensitivity of polyamine metabolism in the prostatic tumour could be the result of qualitative changes that occurred during transformation.     

Synthesis, conformation, and immunoreactivity of new carrier molecules based on repeated tuftsin-like sequence

Sequential oligopeptides based on a pentapeptide (TKPKG) derived from tuftsin with different lengths were synthesized by stepwise solid phase methodology. These highly soluble oligomers were nontoxic on mouse spleen cells, and other biological data suggested that tuftsin-like properties were also presented. The (TKPKG)n (n=2,4,6,8) oligopeptides were not immunogenic; however, they increased sheep red blood cells (SRBC) antigen specific antibody response in mice, demonstrating their immunostimulatory effect. Chemotactic activity was also found on J774 monocyte cells, while MRC5 fibroblasts were chemotactically nonresponders to the tested forms of tuftsin. These oligomers showed unordered and flexible structure by CD measurements, confirmed by computer modeling studies indicating also a fairly good accessibility of the epsilon-amino group of each lysine residue. Data suggest that these new oligotuftsin derivatives can be considered as promising carriers for synthetic vaccine.     

Synthesis of peptide nucleic acid oligomers carrying 5-methylcytosine derivatives by postsynthetic substitution

Summary The preparation of the thymine peptide nucleic acid (PNA) monomer carrying a 2-nitrophenyl group in position 4 is described. This monomer is incorporated into PNA oligomers and reacted with amines to yield PNA oligomers carrying 5-methylcytosine derivatives. During the deprotection-modification step two side reactions were detected: degradation of PNA oligomer from theN-terminal residue and modification ofN ⁴-tert-butylbenzoyl cytosine residue. Protection of theN-terminal position and the use ofN ⁴-acetyl group for the protection of cytosine eliminate these side reactions.     

Conformation and properties of hammerhead-type RNA enzymes

We designed a hammerhead-type RNA enzyme system which consists of three ribooligonucleotide strands (1-3), synthesized these oligomers and their analogues, and examined conformation and properties of the RNA complexes. Imino proton NMR spectra of the complexes were measured and the signals were assigned by comparison with the spectra of some model duplexes. Examination of a complex containing a G----I mutation (Y = I) revealed that the 2-amino group of the third guanosine residue in the loop 1 (L1) plays an important role for maintaining both the activity and loop conformation.     

Substitution of the GalNAc-α-O-Thr¹¹ residue in drosocin with O-linked glyco-peptoid residue: effect on antibacterial activity and conformational change

One of the obvious disadvantages of natural peptides is their liability to proteases. Among the several solutions for this issue, peptoids or oligomers of N-substituted glycine have emerged as a promising tool that may enhance the stability of proteolysis-susceptible natural peptides. We have synthesized the drosocin and its glyco-peptoid analogues linked O-GalNAc at the Thr(11) residue. One of our glyco-peptoid analogues showed an increased antibacterial activity by the modification of the Thr(11) residue with glyco-peptoid. Structure-activity relationship studies revealed that the antibacterial activity by glyco-peptoid drosocin requires three key elements: free hydroxyl group on the carbohydrate moiety, γ-methyl group of the Thr(11) residue derivative and (S)-configuration over (R)-configuration.     

Degradation by the 2',5'-phosphodiesterase activity of mouse cells requires the presence of a ribo hydroxyl group in the penultimate position of the oligonucleotide substrate

A series of 9-beta-D-xylofuranosyladenine (xyloA or xyloadenosine) substituted analogs of 2-5A core trimer and tetramer were examined for their ability to be degraded by the 2',5'-phosphodiesterase activity of cytoplasmic extracts of mouse L cells. Two distinct groups of xyloA-substituted analogs could be readily discriminated. The first group contained xyloadenosine at the 2'-termini and included A2'p5'A2'p5'(xyloA) and A2'p5'A2'p5'A2'p5'(xyloA). These oligomers behaved as did their parent oligoadenylates in that they were equally sensitive to degradation by the 2',5'-phosphodiesterase activity. The second group of oligonucleotides bore a xyloadenosine residue in the penultimate nucleotide residues of the oligomers and included A2'p5'(xyloA)2'p5'(xyloA), (xyloA)2'p5'(xyloA)2'p5'(xyloA), A2'p5'A2'p5'(xyloA)2'p5'(xyloA) and (xyloA)2'p5' (xyloA)2'p5'(xyloA)2'p5'(xyloA). This group was quite resistant to 2',5'-phosphodiesterase activity. In all, the findings demonstrate that the ribo configuration 3'-hydroxyl group in the penultimate nucleotide of the oligonucleotide substrate is a prerequisite for the 2',5'-phosphodiesterase activity.     

Long-chain polyamines (oligoamines) exhibit strong cytotoxicities against human prostate cancer cells

alpha N,(omega)N-bis(ethyl) octamine SL-11160, decamine SL-11159, dodecamine SL-11226, and tetradecamine SL-11175 were chemically synthesized. We called this class of compounds 'oligoamines'. In these compounds, each -NH(2)(+) residue is separated by four CH(2) residues. trans-Unsaturation was also introduced into the center of the oligoamine chain resulting in the trans-octamine SL-11158, trans-decamine SL-11144, trans-dodecamine SL-11172 and trans-tetradecamine SL-11227. cis-Unsaturation gave the cis-octamine SL-11157 and cis-decamine SL-11150. When assayed for their growth inhibitory effect against four human prostate cancer cell lines LnCap, DU-145, DuPro, and PC-3 by a MTT assay, the ID(50) values were less than 1 microM in all four cell lines. On day 6 of treatment, 2 microM SL-11159, SL-11144 and SL-11175 killed over five logs of DuPro cells while SL-11172 killed over four logs as determined by a colony forming efficiency (CFE) assay. In addition, SL-11159, SL-11226 and SL-11227 killed four logs of PC-3 cells. PC-3 cells are generally resistant to shorter chain polyamine analogues. Such a level of cytotoxicity in any of the prostate tumor cell lines has not been observed for any other polyamine analogues tested thus far. The DU-145 cell line was too sensitive to oligoamines to perform a CFE analysis and the DuPro cell line was too sensitive to SL-11227 treatment to obtain reproducible CFE data. Interestingly, all 10 oligoamines were efficient DNA aggregators in a cell-free system and their cytotoxicities generally parallel their capacities to aggregate DNA.