Oligomers In Solution Research Articles

High power amplified spontaneous emission from an oligomer in solution

The laser action from a conductive oligomer 9,9,9′,9′,9″,9″-hexakis(octyl)-2,7′,2′,7″-trifluorene (HOTF) has been demonstrated in this study. First absorption spectra were studied for HOTF in benzene under a wide range of concentrations. The spectra showed that there was only one peak at 355nm under a wide range of concentrations indicating the absence of dimerization. The fluorescence spectra for low concentrations showed two peaks, at 390nm and 410nm, which could be attributed to the monomer and the excimer. At higher concentrations, the peak at 390nm almost vanished and the dominant peak was at 410nm with a hump at 435nm. Laser action was tested in a transverse pumping configuration where the conducting oligomer was pumped by laser pulses from the third harmonic of an Nd:YAG laser (355nm). It could be seen that there were two amplified spontaneous emission (ASE) peaks, at 390 and 410nm. These peaks could be attributed to the monomer and excimer of the HOTF oligomer; but, even after our best efforts, we were not able observe the ASE peak at 435nm corresponding to the hump in the fluorescence spectra. The power of ASE and the photo-chemical stability were remarkably high. This trend for the oligomer is entirely different from its conjugated polymer counterpart poly(9,9-dioctylfluorenyl-2,7-diyl) (PFO). This is perhaps the first report on ASE from an excimeric state of the conjugated oligomer HOTF in liquid solution.

Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30.

PhoPop5 and PhoRpp30 in the hyperthermophilic archaeon Pyrococcus horikoshii, homologues of human ribonuclease P (RNase P) proteins hPop5 and Rpp30, respectively, fold into a heterotetramer [PhoRpp30-(PhoPop5)2-PhoRpp30], which plays a crucial role in the activation of RNase P RNA (PhopRNA). Here, we examined the functional implication of PhoPop5 and PhoRpp30 in the tetramer. Surface plasmon resonance (SPR) analysis revealed that the tetramer strongly interacts with an oligonucleotide including the nucleotide sequence of a stem-loop SL3 in PhopRNA. In contrast, PhoPop5 had markedly reduced affinity to SL3, whereas PhoRpp30 had little affinity to SL3. SPR studies of PhoPop5 mutants further revealed that the C-terminal helix (α4) in PhoPop5 functions as a molecular recognition element for SL3. Moreover, gel filtration indicated that PhoRpp30 exists as a monomer, whereas PhoPop5 is an oligomer in solution, suggesting that PhoRpp30 assists PhoPop5 in attaining a functionally active conformation by shielding hydrophobic surfaces of PhoPop5. These results, together with available data, allow us to generate a structural and mechanistic model for the PhopRNA activation by PhoPop5 and PhoRpp30, in which the two C-terminal helices (α4) of PhoPop5 in the tetramer whose formation is assisted by PhoRpp30 act as binding elements and bridge SL3 and SL16 in PhopRNA.

Successive Stages of Amyloid-β Self-Assembly Characterized by Solid-State Nuclear Magnetic Resonance with Dynamic Nuclear Polarization.

Self-assembly of amyloid-β (Aβ) peptides in human brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Amyloid fibrils, whose structures have been extensively characterized by solid state nuclear magnetic resonance (ssNMR) and other methods, are the thermodynamic end point of Aβ self-assembly. Oligomeric and protofibrillar assemblies, whose structures are less well-understood, are also observed as intermediates in the assembly process in vitro and have been implicated as important neurotoxic species in AD. We report experiments in which the structural evolution of 40-residue Aβ (Aβ40) is monitored by ssNMR measurements on frozen solutions prepared at four successive stages of the self-assembly process. Measurements on transient intermediates are enabled by ssNMR signal enhancements from dynamic nuclear polarization (DNP) at temperatures below 30 K. DNP-enhanced ssNMR data reveal a monotonic increase in conformational order from an initial state comprised primarily of monomers and small oligomers in solution at high pH, to larger oligomers near neutral pH, to metastable protofibrils, and finally to fibrils. Surprisingly, the predominant molecular conformation, indicated by (13)C NMR chemical shifts and by side chain contacts between F19 and L34 residues, is qualitatively similar at all stages. However, the in-register parallel β-sheet supramolecular structure, indicated by intermolecular (13)C spin polarization transfers, does not develop before the fibril stage. This work represents the first application of DNP-enhanced ssNMR to the characterization of peptide or protein self-assembly intermediates.

Hydration, Orientation, and Conformation of Methylglyoxal at the Air-Water Interface.

Aqueous-phase processing of methylglyoxal (MG) has been suggested to constitute an important source of secondary organic aerosol (SOA). The uptake of MG to aqueous particles is higher than expected because its carbonyl moieties can hydrate to form geminal diols, as well as because MG and its hydration products can undergo aldol condensation reactions to form larger oligomers in solution. MG is known to be surface active, but an improved description of its surface behavior is crucial to understanding MG-SOA formation. These studies investigate MG adsorption, focusing on its hydration state at the air-water interface, using a combined experimental and theoretical approach that involves vibrational sum frequency spectroscopy, molecular dynamics simulations, and density functional theory calculations. Together, the experimental and theoretical data show that MG exists predominantly in a singly hydrated state (diol) at the interface, with a diol-tetrol ratio at the surface higher than that for the bulk. In addition to exhibiting a strong surface activity, we find that MG significantly perturbs the water structure at the interface. The results have implications for understanding the atmospheric fate of methylglyoxal.

Baicalin Inhibits the Lethality of Ricin in Mice by Inducing Protein Oligomerization

Toxic ribosome-inactivating proteins abolish cell viability by inhibiting protein synthesis. Ricin, a member of these lethal proteins, is a potential bioterrorism agent. Despite the grave challenge posed by these toxins to public health, post-exposure treatment for intoxication caused by these agents currently is unavailable. In this study, we report the identification of baicalin extracted from Chinese herbal medicine as a compound capable of inhibiting the activity of ricin. More importantly, post-exposure treatment with baicalin significantly increased the survival of mice poisoned by ricin. We determined the mechanism of action of baicalin by solving the crystal structure of its complex with the A chain of ricin (RTA) at 2.2 Å resolution, which revealed that baicalin interacts with two RTA molecules at a novel binding site by hydrogen bond networks and electrostatic force interactions, suggesting its role as molecular glue of the RTA. Further biochemical and biophysical analyses validated the amino acids directly involved in binding the inhibitor, which is consistent with the hypothesis that baicalin exerts its inhibitory effects by inducing RTA to form oligomers in solution, a mechanism that is distinctly different from previously reported inhibitors. This work offers promising leads for the development of therapeutics against ricin and probably other ribosome-inactivating proteins.

Extended piperidine-piperidinone protein interface mimics.

Minimalist structures, H and I, were designed as protein interface mimics. Attributes of these chemotypes are (i) greater rigidity than conventional peptides, (ii) chiral and nonplanar heterocyclic backbones that are less prone to the hydrophobic aggregation effects, and (iii) potential to be prepared with a variety of side chains corresponding to natural amino acids. Intermediates, however, in the oligo(pyrrolidinone-piperidine)s H syntheses were vulnerable to epimerization. The origins of this epimerization were determined, then the study was focused on oligo(piperidinone-piperidine) compounds I. Mimics I were prepared via iterative couplings; a penta(piperidinone-piperidine) was prepared in this way. A series of lower homologues of this pentamer were crystallized and studied (single crystal X-ray), and four of them were used in a circular dichroism (CD) study. Thus, an estimate of 36 Å for the N-to-C distance of a typical conformation of the penta(piperidinone-piperidine) was made. CD spectra of four progressively longer oligomers allowed assignment of elipticity changes around 300 nm that can be attributed to increased conformational ordering of the longer oligomers in solution.

Abiotic ligation of DNA oligomers templated by their liquid crystal ordering.

It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly. In mixtures of oligomers with various degree of complementarity, liquid crystal microdomains are formed via the selective aggregation of those oligomers that have a sufficient degree of duplexing and propensity for physical polymerization. Here we show that such domains act as fluid and permeable microreactors in which the order-stabilized molecular contacts between duplex terminals serve as physical templates for their chemical ligation. In the presence of abiotic condensing agents, liquid crystal ordering markedly enhances ligation efficacy, thereby enhancing its own phase stability. The coupling between order-templated ligation and selectivity provided by supramolecular ordering enables an autocatalytic cycle favouring the growth of DNA chains, up to biologically relevant lengths, from few-base long oligomers. This finding suggests a novel scenario for the abiotic origin of nucleic acids.

The Oligomeric Outer Dynein Arm Assembly Factor CCDC103 Is Tightly Integrated within the Ciliary Axoneme and Exhibits Periodic Binding to Microtubules

CCDC103 is an ∼29-kDa protein consisting of a central RPAP3_C domain flanked by N- and C-terminal coiled coils. Defects in CCDC103 lead to primary ciliary dyskinesia caused by the loss of outer dynein arms. This protein is present along the entire length of the ciliary axoneme and does not require other dynein or docking complex components for its integration. Unlike other known dynein assembly factors within the axoneme, CCDC103 is not solubilized by 0.6 M NaCl and requires more chaotropic conditions, such as 0.5 M KI. Alternatively, it can be extracted using 0.3% sarkosyl. CCDC103 forms stable dimers and other oligomers in solution through interactions involving the central domain. The smallest particle observed by dynamic light scattering has a hydrodynamic diameter of ∼25 nm. Furthermore, CCDC103 binds microtubules directly, forming ∼9-nm diameter particles that exhibit a 12-nm spacing on the microtubule lattice, suggesting that there may be two CCDC103 units per outer arm dynein repeat. Although the outer dynein arm docking complex is necessary to form arrays of dyneins along microtubules, it is not sufficient to set up a single array in a precise location on each axonemal doublet. We propose that CCDC103 helps generate a high-affinity site on the doublets for outer arm assembly, either through direct interactions or indirectly, perhaps by modifying the underlying microtubule lattice.

In situ imidazole activation of ribonucleotides for abiotic RNA oligomerization reactions.

The hypothesis that RNA played a significant role in the origin of life requires effective and efficient abiotic pathways to produce RNA oligomers. The most successful abiotic oligomerization reactions to date have utilized high-energy, modified, or pre-activated ribonucleotides to generate strands of RNA up to 50-mers in length. In spite of their success, these modifications and pre-activation reactions significantly alter the ribonucleotides in ways that are highly unlikely to have occurred on a prebiotic Earth. This research seeks to address this problem by exploring an aqueous based method for activating the canonical ribonucleotides in situ using 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and imidazole. The reactions were run with and without a montmorillonite clay catalyst and compared to reactions that used ribonucleotides that were pre-activated with imidazole. The effects of pH and ribonucleotide concentration were also investigated. The results demonstrate the ability of in situ activation of ribonucleotides to generate linear RNA oligomers in solution, providing an alternative route to produce RNA for use in prebiotic Earth scenarios.

π-Delocalization and the vibrational spectroscopy of conjugated materials: computational insights on Raman frequency dispersion in thiophene, furan, and pyrrole oligomers.

The symmetric C═C stretching frequency (ν(Я)) of conjugated polymers and oligomers is a sensitive spectroscopic reporter of molecular structure and material morphologies; however, thorough understanding of how structure affects this frequency is lacking because computational investigations of this relationship have been undertaken with limited approaches. We present a comprehensive computational investigation of the structure-dependent Raman spectroscopy of oligothiophenes, oligofurans, and oligopyrroles in their ground electronic states using density functional theory. We assessed how various functionals (BLYP, B3LYP, BHLYP, and CAM-B3LYP) impact predictions of length-dependent trends in ν(Я). The amount of Hartree-Fock exchange in a functional is critical for accurately treating π-delocalization and polarizability and hence the structure-dependent Raman behavior. BLYP and B3LYP fail to accurately predict trends in ν(Я) with oligomer length because they over-represent delocalization; in contrast, the range-corrected CAM-B3LYP functional produces the same trends observed experimentally for oligomers in solution and in the solid phase. Through comparisons with a simple mechanical model, we demonstrate that the length- and conformation-dependent spectroscopy of oligothiophenes results from a delicate balance between delocalization-induced softening of ν(Я) and the coupling of oscillators that increase ν(Я). These findings are used to address how variations in inter- and intramolecular order impact the Raman spectroscopy of polythiophenes.

Tetrahydrohyperforin: a neuroprotective modified natural compound against Alzheimer's disease.

According to the World Health Organization (WHO), a total of 35.6 million cases of dementia were estimated in 2010, with close to 7.7 million new cases each year. In 2008, WHO declared dementia a priority condition. 90% of all dementia cases are considered to be Alzheimer's disease (AD). Therefore, great effort was made to understand the etiology of the disease and stop or slow down AD progression.

Microtubule Networks Modulate Cellular Susceptibility to Aβ-Mediated Toxicity

Alzheimer's disease (AD) is a fatal neurodegenerative disorder that is the most common cause of dementia. The self-assembly of the β-amyloid peptide (Aβ) into ordered aggregates, including oligomers and fibrils, is a major hallmark of AD. As we age, significant alterations in our cellular structure, with implications for cellular mechanics, occur. An example of such changes are alterations in the structure of microtubules within cells. As aging is the largest risk factor for the development of AD, we investigated the role of microtubule structure on a cell's ability to cope with exposure to Aβ. Microtubules in GT1-7 cells were systematically altered using a variety of microtubule-altering drugs. Nocodazole and cholchicine were used to disrupt microtubules; paclitaxel was used to stabilize microtubules. The effectiveness of the drugs to change microtubule structure was confirmed by fluorescence microscopy and mechanical measurements using an atomic force microscope. Control cells and cells with altered microtubule structure were then exposed to monomeric and oligomeric solutions of Aβ, as confirmed by several assays. Next, we determined the extent of Aβ binding to cells using flow cytometry, cell death using a variety of toxicity assays, and Aβ-induced changes in cell mechanical properties. We found that altering microtubule structure had little effect on the ability of Aβ to bind cells. However, Aβ-related toxicity was enhanced when cells had disrupted microtubule networks, indicating that they were more sensitive to exposure to Aβ. Cells that had their microtubule networks chemically stabilized were more resistant to Aβ-related toxicity.

Reactive perfluoropolyoxyalkylene oligomers. II. Isothermal equilibrium on silica gel: Macromolecular aggregation

Abstract It has been demonstrated in a previous work that the adsorption/desorption equilibrium of mono- and bis-methylol terminated perfluoropolyether (PFPE) oligomers is described very well by the classic Langmuir model, though the systems under investigation were not perfectly single-component. More precisely, it has been determined that the affinity vs. the solid phase (silica gel) increases proportionally with the number of functional groups per molecule, while the increase in the molecular weight (i.e. the length of the PFPE chain) exerts an opposite effect. The present study, focused on an in-depth understanding of some anomalies observed during the adsorption/desorption process, indicates that the aggregation in solution of these functional oligomers plays a very important role by ruling the dimension of the real species which are under dynamic equilibrium with the silica gel's active sites. The hypothesis that an over-aggregation is promoted, when oligomers confined inside the pores are considered, adequately describes the apparent irreversibility of the adsorption of bifunctional oligomers. Moreover, experimental evidences indicate that there is also a limiting concentration of di-functional species in a non-confined solution, above which the Langmuir model progressively loses its validity, and the activity of the solid phase progressively diminishes. This unexpected result may be explained on a basis of a similar phenomenology. These two peculiar effects show a different dependence on the concentration, being over-aggregated pores active even at relatively low concentrations, confirming that huge size confinement boosts over-aggregation of solutes. Consistently, monofunctional species that can form only smaller aggregates behave as expected on the basis of the classic Langmuir model without any anomaly.

Characterization of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms reveals hexameric assemblies with increased thermal stability.

Most plants contain two isoforms of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase (Rca), a chloroplast protein that maintains the activity of Rubisco during photosynthesis. The longer (α-) Rca isoform has previously been shown to regulate the activity of Rubisco in response to both the ADP:ATP ratio and redox potential via thioredoxin-f. We have characterized the arrangement of the different spinach (Spinacia oleracea) isoforms in solution, and show how the presence of nucleotides changes the oligomeric state. Although the shorter (β-) isoform from both tobacco (Nicotiana tabacum) and spinach tend to form a range of oligomers in solution, the size of which are relatively unaffected by the addition of nucleotide, the spinach α-isoform assembles as a hexamer in the presence of adenosine 5'-[γ-thio]triphosphate (ATPγS). These hexamers have significantly higher heat stability, and may play a role in optimizing photosynthesis at higher temperatures. Hexamers were also observed for mixtures of the two isoforms, suggesting that the α-isoform can act as a structural scaffold for hexamer formation by the β-isoform. Additionally, it is shown that a variant of the tobacco β-isoform acts in a similar fashion to the α-isoform of spinach, forming thermally stable hexamers in the presence of ATPγS. Both isoforms had similar rates of ATP hydrolysis, suggesting that a propensity for hexamer formation may not necessarily be correlated with activity. Modelling of the hexameric structures suggests that although the N-terminus of Rca forms a highly dynamic, extended structure, the C-terminus is located adjacent to the intersubunit interface.

Structural studies and anticancer activity of a novel class of β-peptides.

Functionalized oligomeric organic compounds with well-defined β-proline scaffold have been synthesized by a cycloadditive oligomerization approach in racemic and enantiopure forms. The structure of the novel β-peptides was investigated by NMR spectroscopic and X-ray methods determining the conformational shapes of the β-proline oligomers in solution and solid states. The main structural elements subject to conformational switches are β-peptide bonds between 5-arylpyrrolidine-2-carboxylic acid units existing in Z/E configurations. The whole library of short β-peptides and intermediate acrylamides has been tested on antiproliferative activity towards the hormone-refractory prostate cancer cell line PC-3 revealing several oligomeric compounds with low micromolar and submicromolar activities. Bromine-substituted dimeric and trimeric acrylamides induced caspase-dependent apoptosis of PC-3 cells through cell-cycle arrest and mitochondrial damage.

Aqueous Phase Oligomerization of Methyl Vinyl Ketone by Atmospheric Radical Reactions

Aqueous phase oxidation reactions in atmospheric particles can yield high molecular weight products and create secondary organic aerosol (SOA) upon droplet evaporation. Oxidation by hydroxyl radicals to create oligomers in solution that form SOA has been previously investigated; however, mixed organic solutions that can initiate radical chemistry have been largely overlooked. In aqueous solution, pyruvic acid (PA), an α-keto acid found in both the gas and aqueous phases in the atmosphere, photolyzes via a radical mechanism. Here, we use this photochemistry of pyruvic acid to trigger oligomerization of methyl vinyl ketone (MVK), an α,β-unsaturated compound generated by the atmospheric oxidation of isoprene. We closely compare the reaction products and mechanism to a recent work in which the radical oligomerization of MVK initiated by hydroxyl radical is studied in depth. Using mass spectrometry, it is shown that the two reactions create oligomers of similar molecular weights, up to m/z 1200 for initial MVK...

Radical polymerization of tetrafluoroethylene that forms a colloid solution and gel of oligomers

As the concentration of tetrafluoroethylene (TFE) in the solvent increases, its polymerization is shown to be accompanied by a transformation of the resulting homogeneous solution of oligomers into a colloid one, which then transforms into gel. The micron-sized colloid particles consist of oligomers and solvent molecules, whose number per TFE unit in the oligomer decreases from 15–20 at the threshold of dense phase formation to 4–6 in a gel. A kinetic model of polymerization was suggested. In this model, the chain propagation is limited by monomer diffusion to the growing macroradical and the chain transfer (oligomer formation and regeneration of the prime radical) is limited by the reaction of the growing macroradical with the solvent molecule. The model that allows for the decrease in the diffusion coefficients with increasing of the oligomer chain length and their local concentration leads to a spatially inhomogeneous molecular mass distribution, with long oligomers accumulated in the vicinity of the macroradical and short ones in the distant zone. The formation of colloid particles and gel occurs when the concentration of long oligomers shaped as rigid rods exceeds the critical value for the dense phase formation and the percolation threshold, respectively. The transition from the initial spatial distribution to the equilibrium distribution described by the phase diagram was considered using the model of viscoelastic separation so that phases retain spatial continuity.

Unprecedented Chain‐Length‐Dependent Conformational Conversion Between 11/9 and 18/16 Helix in α/β‐Hybrid Peptides

Abstractα,β‐Hybrid oligomers of varying lengths with alternating proteogenic α‐amino acid and the rigid β2,3,3‐trisubstituted bicyclic amino acid ABOC residues were studied using both X‐ray crystal and NMR solution structures. While only an 11/9 helix was obtained in the solid state regardless of the length of the oligomers, conformational polymorphism as a chain‐length‐dependent phenomenon was observed in solution. Consistent with DFT calculations, we established that short oligomers adopted an 11/9 helix, whereas an 18/16 helix was favored for longer oligomers in solution. A rapid interconversion between the 11/9 helix and the 18/16 helix occurred for oligomers of intermediate length.

Unprecedented chain-length-dependent conformational conversion between 11/9 and 18/16 helix in α/β-hybrid peptides.

α,β-Hybrid oligomers of varying lengths with alternating proteogenic α-amino acid and the rigid β(2,3,3) -trisubstituted bicyclic amino acid ABOC residues were studied using both X-ray crystal and NMR solution structures. While only an 11/9 helix was obtained in the solid state regardless of the length of the oligomers, conformational polymorphism as a chain-length-dependent phenomenon was observed in solution. Consistent with DFT calculations, we established that short oligomers adopted an 11/9 helix, whereas an 18/16 helix was favored for longer oligomers in solution. A rapid interconversion between the 11/9 helix and the 18/16 helix occurred for oligomers of intermediate length.

Interactions between amyloid-β and Tau fragments promote aberrant aggregates: implications for amyloid toxicity.

We have investigated at the oligomeric level interactions between Aβ(25–35) and Tau(273–284), two important fragments of the amyloid-β and Tau proteins, implicated in Alzheimer’s disease. We are able to directly observe the coaggregation of these two peptides by probing the conformations of early heteroligomers and the macroscopic morphologies of the aggregates. Ion-mobility experiment and theoretical modeling indicate that the interactions of the two fragments affect the self-assembly processes of both peptides. Tau(273–284) shows a high affinity to form heteroligomers with existing Aβ(25–35) monomer and oligomers in solution. The configurations and characteristics of the heteroligomers are determined by whether the population of Aβ(25–35) or Tau(273–284) is dominant. As a result, two types of aggregates are observed in the mixture with distinct morphologies and dimensions from those of pure Aβ(25–35) fibrils. The incorporation of some Tau into β-rich Aβ(25–35) oligomers reduces the aggregation propensity of Aβ(25–35) but does not fully abolish fibril formation. On the other hand, by forming complexes with Aβ(25–35), Tau monomers and dimers can advance to larger oligomers and form granular aggregates. These heteroligomers may contribute to toxicity through loss of normal function of Tau or inherent toxicity of the aggregates themselves.