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Nonribosomal peptides (NRPs) are molecules produced by microorganisms that have a broad spectrum of biological activities and pharmaceutical applications (e.g., antibiotic, immunomodulating, and antitumor activities). One particularity of the NRPs is the biodiversity of their monomers, extending far beyond the 20 proteogenic amino acid residues. Norine, a comprehensive database of NRPs, allowed us to review for the first time the main characteristics of the NRPs and especially their monomer biodiversity. Our analysis highlighted a significant similarity relationship between NRPs synthesized by bacteria and those isolated from metazoa, especially from sponges, supporting the hypothesis that some NRPs isolated from sponges are actually synthesized by symbiotic bacteria rather than by the sponges themselves. A comparison of peptide monomeric compositions as a function of biological activity showed that some monomers are specific to a class of activities. An analysis of the monomer compositions of peptide products predicted from genomic information (metagenomics and high-throughput genome sequencing) or of new peptides detected by mass spectrometry analysis applied to a culture supernatant can provide indications of the origin of a peptide and/or its biological activity. doi: 10.1128/JB.00315-10

The light-organ symbiont Vibrio fischeri releases N-acetylglucosaminyl-l,6-anhydro-N-acetylmuramylalanyl[gamma]- glutamyldiaminopimelylalanine, a disaccharide-tetrapeptide component of peptidoglycan that is referred to here as 'PG monomer.' In contrast, most gram-negative bacteria recycle PG monomer efficiently, and it does not accumulate extracellularly. PG monomer can stimulate normal light-organ morphogenesis in the host squid Euprymna scolopes, resulting in regression of ciliated appendages similar to that triggered by infection with V. fischeri. We examined whether the net release of PG monomers by V. fischeri resulted from lytic transglycosylase activity or from defects in AmpG, the permease through which PG monomers enter the cytoplasm for recycling. An ampG mutant displayed a 100-fold increase in net PG monomer release, indicating that AmpG is functional. The ampG mutation also conferred the uncharacteristic ability to induce light-organ morphogenesis even when placed in a nonmotile flaJ mutant that cannot infect the light-organ crypts. We targeted five potential lytic transglycosylase genes singly and in specific combinations to assess their role in PG monomer release. Combinations of mutations in ltgA, ltgD, and ltgY decreased net PG monomer release, and a triple mutant lacking all three of these genes had little to no accumulation of PG monomers in culture supernatants. This mutant colonized the host as well as the wild type did; however, the mutant-infected squid were more prone to later superinfection by a second V. fischeri strain. We propose that the lack of PG monomer release by this mutant results in less regression of the infection-promoting ciliated appendages, leading to this propensity for superinfection.

Bacillus cereus Fnr is a member of the Crp/Fnr (cyclic AMP-binding protein/fumarate nitrate reduction regulatory protein) family of helix-turn-helix transcriptional regulators. It is essential for the expression of hbl and nhe enterotoxin genes independently of the oxygen tension in the environment. We studied aerobic Fnr binding to target sites in promoters regulating the expression of enterotoxin genes. B. cereus Fnr was overexpressed and purified as either a C-terminal His-tagged ([Fnr.sub.His]) fusion protein or an N-terminal fusion protein tagged with the Strep-tag (IBA BioTAGnology) ([sub.strep]Fnr). Both recombinant Fnr proteins were produced as apoforms (clusterless) and occurred as mixtures of monomers and oligomers in solution. However, [apoFnr.sub.His] was mainly monomeric, while [apo.sub.Strep]Fnr was mainly oligomeric, suggesting that the His-tagged C-terminal extremity may interfere with oligomerization. The oligomeric state of apoStrepFnr was dithiothreitol sensitive, underlining the importance of a disulfide bridge for apoFnr oligomerization. Electrophoretic mobility shift assays showed that monomeric apoFnr, but not oligomeric apoFnr, bound to specific sequences located in the promoter regions of the enterotoxin regulators fnr, resDE, and plcR and the structural genes hbl and nhe. The question of whether apoFnr binding is regulated in vivo by redox-dependent oligomerization is discussed.

The monomer and dimmer acetonitrile anions are examined in order to understand the unusual electronic structure of these species. The atoms in molecules (AIM) analysis has shown the topological variety of the excess electron interacting with acetonitrile molecules, which has manifested itself as charge concentrations, pseudo-atoms and covalent bonds.

Molecular beacon (MB) DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, are used for real-time probing of DNA sequences. The additional pyrene monomer has resulted in substantial increases in the excimer emission intensities, quantum yields and excited-state lifetimes of the hybridized MBs.

The femtosecond pump-probe spectroscopic study results for the electronic structure and dynamics of isolated adenine, thymine dimers and the adenine-thymine base pair are presented. The observation from the photoelectron spectra indicate short-lived [pi][pi]* and n[pi]* perturbed populations in the hydrogen-bound dimers as compared to the monomers.

CIpB and Hsp104, members of the AAA+ superfamily of proteins, protect cells from the devastating effects of protein inactivation and aggregation that arise after extreme heat stress. They exist as a hexameric ring and contain two nucleotide-binding sites per monomer. CIpB and Hsp104 are able to dissolve protein aggregates in conjunction with the DnaK/Hsp70 chaperone system, although the roles of the individual chaperones in disaggregation are not well understood. In the absence of the DnaK/Hsp70 system, CIpB and Hsp104 alone are able to perform protein remodeling when their ATPase activity is asymmetrically slowed either by providing a mixture of ATP and ATP[gamma]S, a nonphysiological and slowly hydrolyzed ATP analog, or by inactivating one of the two nucleotide-binding domains by mutation. To gain insight into the roles of CIpB and the DnaK system in protein remodeling, we tested whether there was a further stimulation by the DnaK chaperone system under conditions that elicited remodeling activity by CIpB alone. Our results demonstrate that CIpB and the DnaK system act synergistically to remodel proteins and dissolve aggregates. The results further show that ATP is required and that both nucleotide-binding sites of CIpB must be able to hydrolyze ATP to permit functional collaboration between CIpB and the DnaK system.

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of [(A[[beta].sub.16-22]).sub.n] by adding a monomer to a preformed [(A[[beta].sub.16-22]).sub.n-1] (n = 4-6) oligomer in which the peptides are arranged in an antiparallel [beta]-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 [micro]s, show that the oligomer grows by a two-stage dock-lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid ([approximately equal to] 50 ns) first dock stage in which the [beta]-strand content of the monomer increases substantially from a low initial value, in the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when n = 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock-lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.

A set of monolithic stationary phases representing a broad span of monomers and porogens have been characterized directly in their capillary chromatographic format by computational assessment of their pore structure from transmission electron micrographs obtained after in situ embedment of the monoliths in contrast resin, followed by dissolution of the fused-silica tubing, further encasement of the resin-embedded monolith, and microtomy. This technique has been compared to mercury intrusion, a more conventional technique for macroporosity estimation. Supplementing the embedding resin by lead methacrylate gave a negative staining, and the resulting micrographs showed a good contrast between the polymeric monoliths and the embedding resin that allowed studies on the pore formation and polymer development. The technique was also applied to a commercial monolithic silica column.

The role of N-terminus and its microenvironment is examined in determining enzyme stability and catalysis using human placental alkaline phosphatase (PLAP) and tissue-nonspecific alkaline phosphatase (TNAP) as examples. Results reveal that N-terminal alpha-helical folding is very important for structural stability of second monomer in TNAP than in PLAP.

In this report, we introduce a new entry of high-performance polymer-based monolithic capillary column for mainly small molecules. This capillary column was prepared using a newly introduced epoxy monomer with diamines. Simply heat-induced polycondensation in an appropriate porogenic solvent afforded a really homogeneous co-continuous monolithic structure having submicrometer-size skeletons with micrometer-size throughpores. We were also able to prepare chiral monolithic columns using a chiral epoxy monomer as well as a chiral diamine. A 21.5-cm-long, 100-[micro]m-i.d. column afforded up to 40 000 theoretical plate numbers (N) for alkylbenzenes in 60% aqueous acetonitrile as a reversed-phasemode stationary phase. Due to a quite low column pressure drop, a 150-cm-long column was prepared. This long column afforded up to 200 000 plates for alkylbenzenes with only a 4-MPa column pressure drop. In contrast, in 100% acetonitrile, this column has 'HILIC' property to show up to 60 000 plates for methanol with a 17.5-cm-long column. In this mode, we were able to separate nucleic acids. In addition, we have prepared a chiral column with both of the chiral epoxy monomers and an amine. This column was able to chirally discriminate a racemic alcohol in a reversed-phase mode.

We present a robust and simple method for direct, label-free PCR product quantification using an integrated microelectronic sensor. The field-effect sensor can sequentially detect the intrinsic charge of multiple unprocessed PCR products and does not require sample processing or additional reagents in the PCR mixture. The sensor measures nucleic acid concentration in the PCR relevant range and specifically detects the PCR products over reagents such as Taq polymerase and nucleotide monomers. The sensor can monitor the product concentration at various stages of PCR and can generate a readout that resembles that of a real-time fluorescent measurement using an intercalating dye but without its potential inhibition artifacts. The device is mass-produced using standard semiconductor processes, can be reused for months, and integrates all sensing components directly on-chip. As such, our approach establishes a foundation for the direct integration of PCR-based in vitro biotechnologies with microelectronics.

A simple strategy is proposed to assess the propensity of a given monomer to follow or not follow a particular helical scheme and to study helix reversal phenomena within helical oligomers. It consists of placing a monomer having a low helix propensity between two conformationally stable helical segments. Helix reversion then occurs preferentially at the site of this monomer, leading to the formation of isomers having P (right-handed) or M (left-handed) helicities at each of the two helical segments. The proportion between the P-P/M-M and P-M isomers is indicative of the stereochemical relations between the inserted monomer and the helical frame. Thus, xylylene or carboxylic acid anhydride spacers have been introduced between two helical oligoamides of 8-amino-2-quinolinecarboxylic acid. Both these spacers presumably lack some of the structural features that confer quinoline units with a high helix propensity. Only one species is observed in solution in the case of an anhydride spacer. This species was shown by x-ray crystallography to be a racemic mixture of P-P and M-M helices. Unexpectedly, the anhydride is consistently incorporated within helical oligoamides. For the xylylene spacer, the P-P/M-M racemate and P-M meso compound are in equal proportions in chloroform, showing that this spacer does not have a propensity to adopt any helical conformation in this solvent. However, the equilibria between the various isomers are shifted in toluene, where one species largely prevails. This species was shown by x-ray crystallography to be the P-P/M-M racemate. Molecular dynamics simulations are consistent with these solution data. conformation analysis | folding | helices

Aiming at enhancing the advantages of traditional molecularly imprinted polymers (MIPs) for chemical sensing, a new MIP design approach introducing an internal heavy atom in their polymeric structure is described. Based on the heavy-atom effect, the novel polymer allows one to perform room-temperature phosphorescence (RTP) transduction of the analyte. The synergic combination of a tailor-made MIP recognition with a selective RTP detection is a novel concept for optosensing devices which is assessed here for simple and highly selective determination of trace amounts of fluoranthene in water. The noncovalent MIP was synthesized using the laboratory-synthesized tetraiodobisphenol A as one of the polymeric precursors and fluoranthene as template. In the presence of an oxygen scavenger, the iodide included in the polymeric structure induced efficient RTP emission from the analyte, once recognized by the MIP. The developed optosensing system has demonstrated a high specificity for fluoranthene against other polycyclic aromatic hydrocarbons. Detection limit for the target molecule was 35 ng/L (5-mL sample injections), and the linear range extended above 100 [micro]g/L of the analyte. The polymer can be easily regenerated for subsequent sample injections (at least up to 450 cycles) with acetonitrile. The synthesized sensing material showed good stability for at least 6 months after preparation. The feasibility of monitoring fluoranthene in real samples was successfully evaluated through the analysis of five spiked fiver water samples.

Ionic liquids (ILs) are a class of nonmolecular solvents in which the cation/anion combination can be easily tuned to provide desired chemical and physical properties. When used as stationary phases in gas-liquid chromatography, ionic liquids exhibit dual nature retention selectivity. That is, they are able to separate polar molecules such as a polar stationary phase and nonpolar molecules such as a nonpolar stationary phase. However, issues such as optimization of the wetting ability of the ionic liquid on fused-silica capillaries, the maximum operating temperatures of the stationary phases, and nonuniform film thickness on the wall of the capillary at high temperatures have limited their use in gas chromatography. As described in this paper, these limitations are overcome by cross-linking a new class of ionic liquid monomers by free radical reactions to provide a more durable and robust stationary phase. By lightly cross-linking the ionic liquid stationary phase using a small amount of free radical initiator, high-efficiency capillary columns were produced that are able to endure high temperatures with little column bleed. Two types of cross-linked IL stationary phases are developed. A partially cross-linked stationary phase allows for high-efficiency separations up to temperatures of ~280[degrees]C. However, by creating a more highly cross-linked stationary phase of geminal dicationic ILs, exclusively, an increase in efficiency is observed at high temperatures allowing for its use over 350[degrees]C. In addition, through the use of solvation thermodynamics and interaction parameters, it was shown that the cross-linking/immobilization of the ionic liquid does not affect the selectivity of the stationary phase thereby preserving its dual nature retention behavior.

The SAR11 clade is one of the most abundant bacterial phylogenetic groups in the ocean. Existing data suggests that SAR11 bacteria do not utilize various components of the dissolved organic matter (DOM) pool equally and might be more important to the flux of low-molecular-weight monomers than to that of high-molecular-weight polymers.

Abstract -- A procedure was developed for the quantitative determination of free monomers in a copolymer of methacrylic acid and butyl methacrylate used in the medical industry for manufacturing antiseptic [...]

Free radical polymerization kinetics of diallyl terephthalate in bulk was investigated in a wide temperature range from 50[degrees]C to 150[degrees]C with four different peroxide initiators. Conversion points were measured using Fourier Transform Infrared (FTIR) measurements. The initiator efficiencies and the initiator decomposition rate constants were evaluated from special experiments, applying the theory of dead end polymerization. In addition, the ratios between the degradative and the effective kinetic rate constants to propagation rate constants were obtained from molecular weight measurements at various initiator concentrations. The ratio of chemically controlled termination and propagation rate constant [k.sub.pc.sup.2]/[k.sub.tc] of the polymerization system was obtained using the initial rates of polymerization and the number average molecular weight data between 0.25 * [10.sup.-3] and 15.7 * [10.sup.-3] L [mol.sup.-1] [s.sup.-1]. The glass transition temperature of the polymer, 191[degrees]C, was measured by the Alternating Differential Scanning Calorimetry (ADSC) technique. Computed conversions from the developed kinetic model were in good agreement with the conversion and molecular weight measured data. The values of diffusion controlled propagation and termination rate constants [k.sub.td0] and [k.sub.pd0] with clear and physical meaning were the only two parameters obtained from the developed kinetic model fitting. Polym. Eng. Sci. 44:2005-2018, 2004. [c] 2004 Society of Plastics Engineers., INTRODUCTION Diallyl terephthalate (DAT), an isomer of diallyl phthalate (DAP) monomer, is considered a promising engineering plastic material. The monomer has low toxicity and high reactivity for homopolymerization and copolymerization [...]

The removal of spent initiator, excess initiator and unbound monomer from newly synthesized polypropylene-graft-maleic anhydride (PP-g-MA) has typically been carried out using Soxhlet extraction. Standard solvents used in the Soxhlet process are xylene, toluene, acetone or methanol. These chemicals are not only hazardous to some degree, but also lead to undesirable maleic anhydride (MA) ring opening. This paper establishes that supercritical carbon dioxide (scC[O.sub.2]) extraction of residuals prevents anhydride ring opening and eliminates the need for post-extraction vacuum-drying of the copolymer product. An added benefit of this innovative process is that environmentally friendly carbon dioxide (C[O.sub.2]) is used in place of harmful solvents. The successful extraction of the residuals is established by thermogravimetric analysis (TGA). whereas FTIR spectroscopy is used to compare the anhydride content of Soxhlet-extracted PP-g-MA to that of scC[O.sub.2]-extracted copolymer. Polym. Eng. Sci. 44:1636-1641, 2004. © 2004 Society of Plastics Engineers., INTRODUCTION The use of supercritical fluids as an extraction medium has been successful in many applications as a replacement for liquid solvents and as a means of performing difficult separations. [...]

A highly active, monomeric chorismate mutase, obtained by topological redesign of a dimeric helical bundle enzyme from Methanococcus jannaschii, was investigated by NMR and various other biochemical techniques, including H/D exchange. Although structural disorder is generally considered to be incompatible with efficient catalysis, the monomer, unlike its natural counterpart, unexpectedly possesses all of the characteristics of a molten globule. Global conformational ordering, observed upon binding of a transition state analog, indicates that folding can be coupled to catalysis with minimal energetic penalty. These results support the suggestion that many modern enzymes might have evolved from molten globule precursors. Insofar as their structural plasticity confers relaxed substrate specificity and/or catalytic promiscuity, molten globules may also be attractive starting points for the evolution of new catalysts in the laboratory.

The possibility of using triynes [R(C triple bond CH)3] as monomer units to assemble hyperbranched polyynes is explored. A group of hyperbranched polyynes (hb-PYs) is prepared through structural design and reaction control, which are soluble, emissive, refractive, thermally curable, peripherally functionalizable, and molecularly metallizable.

First through fourth generation (G1-G4) dendronized macromonomers with a methyleneoxycarbonyl spacer between the polymerizable group and dendritic side chain (dendron) were synthesized, and their polymerization behavior to the dendronized polymers were investigated by heating the monomers to 55 degree C without intentional addition of initiator. Both structure and dynamics were investigated by DSC, X-ray diffraction, and dynamic mechanical measurements.

The total synthesis of the lichen-derived antitumor agent hybocarpone and related compounds are studied. Direct access to the hybocarpone skeleton is possible by oxidative dimerization of the corresponding naphthazarin monomer employing CAN as the oxidant.

Measurements of chemical exchange events in the crystalline polycarbonate monomer 4,4'-isopropylidenediphenol (bisphenol A, BPA) via 2D 13C solid-state NMR shows slow, large-amplitude aromatic ring orientations. Experiments with multiple exchange times show that ring flips occur in all of the three unique conformers found in the crystalline unit cell of this compound, but in specific cases, two of the three unique molecules actually switch conformations.

Full account of the total synthesis and absolute stereo chemical assignment of (+)-torreyanic acid is reported. Thermolysis experiments are conducted on a model dimer based on the torreyanic acid core structure and facile retro Diels-Alder reaction processes and equilibration of diastereomeric 2H- pyrans is observed.

The changes in the structural, vibrational, bonding, and electronic properties of small clusters of the group III nitrides when an electron is added to the neutral clusters are described. The atomic charge analysis suggests that the added electron is located over the metallic atoms in dimers and trimers and equally shared by metal and nitrogen atoms in monomers.

The monomer radical and the dimer radical cation of cyanopyridinium derivatives was studied by absorption and electron spin resonance (ESR) spectroscopies at room temperature. The results indicated that the formation of monomer radicals and dimer radical cations from the same cyanopyridinium cations by photoinduced electron transfer in acetonitrile (ACN) at room temperature.

The ultrafast fluorescence up-conversion behaviors of a series of hemicyanine dyes, including monomer and dimmers, are studied. The fluorescence decay curves of these dyes can be well fitted by the sum of several exponential decays in the shorter wavelengths and by the sum of the exponential rises with decays in the longer wavelengths.

Research has been conducted on the aldose reductase (AR), a NADPH-dependent enzyme causing diabetic complications. The results of the interactions of R- and S-isomers with AR under physiological conditions in the attempt to elucidate the inhibition modes are discussed.

Evidence of monomer contribution to static magnetic birefringence in magnetic fluids is reported experimentally.

Research has been conducted on eotaxin-3 which activates chemokine receptor CCR3. The 3D structure and backbone dynamics of eotaxin-3 that have been determined by NMR spectroscopy are described.

Research has been conducted on the phospholipids hydrolysis by class II phospholipase A (sub)2 (PLA (sub)2) which involves a Ca (super)2+ ion cofactor. The effect of pH on the monomer-dimer equilibrium of Lys49-PLA (sub)2 from the Bothrops jararacussu venom has been investigated.

Research has been conducted on the dimeric Crotalus atrox venom phospholipase. The study of the monomer-dimer equilibrium of the C. atrox venom in solution in the presence of urea and monomeric phosphatidylcholine analogue has been carried out via fluorescence correlation spectroscopy.

Research has been conducted on the monomeric titanocene(III) complex Cp (sub)2 TiPh. The use of this complex in investigating the catalyzed inter- and intramolecular pinacol couplings is discussed.

An interface appeared during the polymerization to form heterogeneous structures in the vicinity of the hydrophobic substrates when a hydrogel was polymerized from its vinyl monomer in water. This substrates effect was found to have a correlation with the surface tension of the hydrophobic surface.

Research is presented concerning the investigation of chromophore aggregation and phenyl group rotation in poly- and oligo-(phenyleneethynylene)s through the use of semiempirical calculations and photophysical measurements.

Individual NO monomers, with adsorption at 4-65K and at low coverages, are imaged at 4K and appear as depressions in the STM images. The low barrier to diffusion, together with its appearance in STM, proves that monomer is weakly chemisorbed.

It has been possible to identify a complex kinetic rate law in a catalytic reaction network where the active monomeric species is in equilibrium with a dimer species. The rate constants can be estimated in cases where transitions between dominant terms in the reaction rate law arise.

Spectroscopic investigations on structure and dynamics of 9(10H) -acridone (AD) and its hydrated clusters were performed. The monomer band in the FE spectrum is extremely weak implying small fluorescence quantum yield; while the cluster bands are stronger hence the quantum yield is more.

A synthesis made of a protected form of (R,R,R,)-2,5-diaminocylohexanecarboxylic acid (DCHC), a monomer, to enable a study of 14-helix formation by short beta-peptides in a water solution is presented. An improved synthesis of protected versions of ACHC itself is also reported.

Research has been conducted on the structure formation and dimerization in the Arc repressor refolding. The investigation of the secondary structure integrity in the Arc refolding transition state has been carried out.

It is possible to systematize experimental data on CO2 frequency shifts obtained for different vibrational modes using a correlation with the square root of the critical temperature. The use of the correlations identified in this research allows an indication of some intervals in which the host material critical temperature can be anticipated.

Research into the energetics of gas-phase tautomerization of both monomers and dimers of the 4-pyridinol and 4(1H)-pyridinone molecules is presented. The hydrogen-bond energies show a strong preference for 4(1H)-pyridinon-containing dimers.

High-frequency voltage pulses at a microelectrode are used to evaluate solution electrogenerated chemiluminescence for molecules of interest for organic light-emitting diodes.

Research has been conducted on the on the quinuclidine-stabilized amido- and azidogallanes. The synthesis of these compounds from the mono- and dichlorogallane quinuclidine adducts is described.

A new study uses gas-phase electron diffraction and quantum chemical studies to investigate the molecular geometry of monomeric and dimeric gold trifluoride.

Research has been conducted on the CC chemokine structures. The use of nuclear magnetic resonance spectroscopy in analyzing the mutants' oligomeric state is described.

A promising new type of monomer in the P-stereospecific synthesis of PS-ODNs has been found in deoxyribonucleoside cyclic N-acylphosphoramidites such as Rp-1 and Sp-1.

Research has been conducted on the TATA-binding protein (TBP). The role of TBP dimerization in transcriptional initiation regulation is discussed.