Changes In Aggregation Behavior Research Articles

Glyphosate metabolism in Tetrahymena thermophila: A shotgun proteomic analysis approach.

Glyphosate is one of the most widely used herbicides in the world. However, because of its overuse and resistance to degradation, high levels of glyphosate residues in the environment are reported. Therefore, this study aimed to investigate the effects of glyphosate on proteomic aspects of Tetrahymena thermophila and their uses as bioindicators of freshwater ecosystem. First, an acute toxicity test was performed to determine the median inhibition concentration (IC50 ). The toxicity test results showed that glyphosate inhibited the growth (proliferation) of T. thermophila. The 96 h-IC50 value of glyphosate was 171 mg L-1 . No visible changes in aggregation behavior and cell morphology were observed under glyphosate exposure. In addition, the effects of low and high dose glyphosate concentrations (77.5mg L-1 , 171 mg L-1 ) on the proteomic changes of T. thermophila was investigated using a label-free shotgun proteomic approach. A total of 3191 proteins were identified, 2791 proteins were expressed in the control, 2651 proteins were expressed in 77.5mg L-1 glyphosates, and 3012 proteins were expressed in 171 mg L-1 glyphosates. Under glyphosate exposure at both low and high dose glyphosate, 400 unique proteins were upregulated. The majority of these proteins was classified as proteins associated with oxidative stress response and intracellular transport indicating the shifts in the internal metabolism. Proteomics revealed that the glyphosate metabolism by T. thermophila is a multi-step process involving several enzymes, which can be divided into four phases, including modification (phase I), conjugation (phase II), transport (phase III), and degradation (phase IV). The accumulation of various biochemical reactions contributes to overall glyphosate resistance. With the proteomics approach, we have found that T. thermophila was equipped with glyphosate detoxification and degradation mechanisms.

Small Molecule: Polymer Blends for N‐type Organic Thin Film Transistors via Bar‐coating in Air

Comprehensive SummaryFabricating n‐type organic thin film transistors (OTFTs) based on small molecules via solution processing under atmospheric conditions remains challenging. Blending small molecules with polymer is an effective strategy to improve the solution processibility and air stability of the resulted devices. In this study, polystyrene was chosen to blend with n‐type small molecule DPP1012‐4F to enhance the continuity of the semiconductor layer and maintain a favorable edge‐on stacking of semiconductors. The introduction of high‐boiling point 1‐chloronaphthalene as a solvent additive in the blending system can reduce the grain boundary defects in the microscopic morphology. These changes in aggregation behavior are confirmed by X‐ray diffraction, atomic force microscopy and polarized optical microscopy analyses. Via bar‐coating of the semiconductor layers in air, the electron mobility of the resulted OTFTs under the optimal condition is 0.73 cm2·V–1·s–1, which is amongst the highest n‐type small molecule‐based OTFTs with active layers prepared in air up to now. These results show a great potential of the blending strategy in industrial roll‐to‐roll manufacture of high‐mobility n‐type OTFTs.

Application of Voltage in Dynamic Light Scattering Particle Size Analysis.

Dynamic light scattering (DLS) is a common method for characterizing the size distribution of polymers, proteins, and other nano- and microparticles. Modern instrumentation permits measurement of particle size as a function of time and/or temperature, but currently there is no simple method for performing DLS particle size distribution measurements in the presence of applied voltage. The ability to perform such measurements would be useful in the development of electroactive, stimuli-responsive polymers for applications such as sensing, soft robotics, and energy storage. Here, a technique using applied voltage coupled with DLS and a temperature ramp to observe changes in aggregation and particle size in thermoresponsive polymers with and without electroactive monomers is presented. The changes in aggregation behavior observed in these experiments were only possible through the combined application of voltage and temperature control. To obtain these results, a potentiostat was connected to a modified cuvette in order to apply voltage to a solution. Changes in polymer particle size were monitored using DLS in the presence of constant voltage. Simultaneously, current data were produced, which could be compared with particle size data, to understand the relationship between current and particle behavior. The polymer poly(N-isopropylacrylamide) (pNIPAM) served as a test polymer for this technique, as pNIPAM's response to temperature is well-studied. Changes in the lower-critical solution temperature (LCST) aggregation behavior of pNIPAM and poly(N-isopropylacrylamide)-block-poly(ferrocenylmethyl methacrylate), an electrochemically active block-copolymer, in the presence of applied voltage are observed. Understanding the mechanisms behind such changes will be important when trying to achieve reversible polymer structures in the presence of applied voltage.

AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches.

Protein aggregation is a phenomenon that has attracted considerable attention within the pharmaceutical industry from both a developability standpoint (to ensure stability of protein formulations) and from a research perspective for neurodegenerative diseases. Experimental identification of aggregation behavior in proteins can be expensive; and hence, the development of accurate computational approaches is crucial. The existing methods for predicting protein aggregation rely mostly on the primary sequence and are typically trained on amyloid-like proteins. However, the training bias toward beta amyloid peptides may worsen prediction accuracy of such models when applied to larger protein systems. Here, we present a novel algorithm to identify aggregation-prone regions in proteins termed "AggScore" that is based entirely on three-dimensional structure input. The method uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins. AggScore can accurately identify aggregation-prone regions in several well-studied proteins and also reliably predict changes in aggregation behavior upon residue mutation. The method is agnostic to an amyloid-specific aggregation context and thus may be applied to globular proteins, small peptides and antibodies.

Changes in aggregation behavior of raw and cooked salted egg yolks during pickling

In this study, we aimed to investigate the changes in gelation behavior of raw (without heating) and cooked (with heating) salted egg yolks during pickling. Results indicated that the decreasing trend in the main peak T22 of raw and cooked salted egg yolks. Cooked salted egg yolks after 28 days of pickling had a higher release of free lipids as visualized using a confocal laser scanning microscope (CLSM). Transmission electron microscope (TEM) micrographs showed that protein granules were distributed together with lipid spheres in raw and cooked salted egg yolks, and the liberated constituents (lipids and proteins) reorganize and aggregate in cooked salted egg yolks after 28 days of pickling. As the pickling proceeded, the soluble protein content and free sulfhydryl content of raw salted egg yolks, the free sulfhydryl content and surface hydrophobicity of cooked salted egg yolks showed an overall increasing trend, followed by significant decrease. The surface hydrophobicity of raw salted egg yolks exhibited an increasing trend. Differential scanning calorimetry (DSC) results demonstrated that salting can stabilize the protein molecules by an increase in denaturation temperatures. Fourier transform infrared spectroscopy (FTIR) revealed that the secondary structures of egg yolk proteins underwent changes, but no difference in protein patterns of either raw or cooked salted egg yolks was observed by SDS–PAGE during pickling. These results suggested that the characteristic gel of salted egg yolks is formed, as the result of multiple interactions between protein molecules and between protein and lipid molecules.

Changes in aggregation behavior of collagen molecules in solution with varying concentrations of acetic acid

A critical aggregation concentration of 0.30–0.50mg/mL was previously obtained for type I collagen at 0.1M acetic acid (AA). In the present study, the aggregation behavior of collagen in solution (0.5mg/mL) in the presence of 0.1–2.0M AA was investigated. Circular dichroism showed that the three helix structure was maintained across the whole AA concentration range. However, the ratio of positive peak intensity over negative peak intensity varied depending on the conformational state of collagen aggregates. Ultra-sensitive differential scanning calorimetry revealed that transition temperatures Tm1 and Tm2 decreased by 8.35°C and 7.80°C, respectively, between 0.1M and 2.0M, indicating a possible relationship between the aggregation state and the thermal effect. The surrounding polarity of collagen molecules in solution containing pyrene was investigated by fluorescence spectroscopy, which demonstrated that disaggregation of collagen aggregates was enhanced with increasing AA concentration. This observation was correlated with changes in collagen fiber size observed by atomic force microscopy. Furthermore, collagen tyrosine residues were blue-shifted in an intrinsic fluorescence spectra, further indicating changes in aggregation behavior with increasing AA concentration. Finally, the dynamic response of collagen molecules to AA was analyzed by two-dimensional correlation fluorescence spectra.

Solvent Tunable Self-Assembly of Amphiphilic Rod–Coil Block Copolymers with Chiral, Helical Polycarbodiimide Segments: Polymeric Nanostructures with Variable Shapes and Sizes

The nanoscale self-assembly of four amphiphilic rod–coil di- and triblock copolymers with chiral, rodlike poly(N-1-phenethyl-N′-methylcarbodiimide) (PPMC) segments and random coil, hydrophilic PEG blocks has been investigated using dynamic light scattering (DLS) and tapping-mode atomic force microscopy (AFM). This self-assembly proved to be highly tunable simply upon altering the concentration and chemical structure of the hydrophilic selective solvent and/or blending the copolymers with polycarbodiimide homopolymer. When spin-coated from dilute (c = 0.5 mg/mL) THF/H2O solutions, these interesting polymers adopted either simple spherical micelles or spherical polymersomes depending on the relative amount of H2O used for dissolution. Switching selective solvent from H2O to MeOH induced changes in aggregation behavior, as evidenced by DLS and AFM, with interesting nanoworm and nanomaggot micelle assemblies observed when spin-coated from dilute THF/MeOH solutions. Blending high-MW PPMC homopolymer with the b...

Real-time visualization of colorimetric probe for pH-sensitive based on poly-(γ-glutamic acid)-functionalized gold nanoparticles

A rapid and simple real-time visualization of colorimetric method for pH-sensitive was development based upon the aggregation of poly-(γ-glutamic acid)-stabilized gold nanoparticles (PGA-AuNPs). The gold nanocrystal seed-mediated approach using cetyltrimethylammonium bromide (CTAB) as a stabilizing surfactant was commonly used to make large quantities of AuNPs. Electrostatic self-assembly technique was used to assemble negatively charged PGA on the surface of positively charged CTAB-capped AuNPs. Results showed that decrease in pH near 5–6 and increase in pH near 8–9 led to the aggregation of PGA-AuNPs. The colorimetric probe showed a sensitive response to pH variation between 1 and 9. The change in aggregation behavior with pH occurred within a narrow range of pH from 5 to 6 (pKa∼4.5–5.5). The decrease in the solution pH gradually converted the side chains of PGA from deprotonate form to protonate form. Such change switching could weaken electrostatic interactions with the modified AuNPs and thus accelerate their release and aggregation. The helix–coil transition of PGA indicated that the aggregation of PGA-AuNPs corresponded to the transition in the secondary structure of the polyacid.

Effect of hydrophilic ionic liquid on aggregation behavior of aqueous solutions of sodium dodecylsulfate (SDS)

This paper delineates the change in aggregation behavior of aqueous sodium dodecylsulfate (SDS), an anionic surfactant upon addition of “hydrophilic” ionic liquid (IL) 3-methy-1-pentylimidazolium tetrafluoroborate in an increase in critical micelle concentration (cmc). The results demonstrate the presence of electrostatic and hydrophobic interactions between the ions of IL and the head group of the surfactant. From the cmc values and their temperature dependence, the thermodynamic parameters, viz. free energy of micellization (ΔGm0) and entropy of micellization (ΔSm0) were evaluated to permit speculation of the interactions existing in the studied aqueous surfactant-IL systems. Further, 1H NMR chemical shift measurements in micelle solutions containing IL have also been carried out. The results obtained are compared with the conclusions drawn from the conductance and fluorescence measurements.

Size-dependent behavior of tuna in an array of fish aggregating devices (FADs)

Several lines of evidence indicate that aggregations of yellowfin tuna associated with floating objects are more frequently composed of small animals than larger ones. Also, the diet of small yellowfin tuna caught at anchored fish aggregating devices (FADs) around Oahu, Hawaii, was found to shift quite rapidly when these fish reached approximately 50 cm FL. In order to test for ontogenetic changes in aggregation behavior, we tagged and released two distinct size classes of yellowfin tuna in an array of anchored FADs around Oahu, Hawaii. Twenty-four yellowfin tuna 30–39 cm FL and 16 yellowfin tuna 63–83 cm FL were tagged with acoustic transmitters and released near anchored FADs equipped with automated acoustic receivers. Fish in the smaller size class stayed about 2.5 times longer at individual FADs than the larger fish (mean 4.05 days vs. 1.65 days) and displayed larger horizontal movements within the array. However, the durations of unassociated phases, residence times in the entire FAD array, percentage of time spent associated with FADs and numbers of movements between FADs did not show any difference between the two size groups. The observed size-dependent behavior is discussed in terms of physiological abilities, diet segregation and anti-predator behavior.

The abiotic formation of TEP under different ocean acidification scenarios

In view of rising atmospheric CO 2 concentrations, the question if the marine biological carbon pump will increase or decrease in efficiency as ocean acidification progresses becomes central for predictions of future atmospheric pCO 2. Aggregation and sinking of aggregates contributes significantly to the flux of carbon to depths and changes in aggregation behavior will have far reaching consequences for the biological pump. The abundance and characteristics of transparent exopolymer particles, TEP, are central in regulating aggregation. We investigated the impact of ocean acidification on the abiotic formation of TEP from their precursors. Our results demonstrate that, contrary to earlier suggestions, ocean acidification as expected in the future ocean has no impact on the equilibrium conditions between TEP and their precursors. However, if the carbonate system is altered by adding acid, which does not simulate the future ocean carbonate system correctly, TEP concentration increases with decreasing pH, presumably due to changes in total alkalinity (TA). This implies that abiotic TEP formation is sensitive to changes in TA, but not pH. The discrepancy in results caused by different experimental approaches emphasizes the fact that acidification experiments do not mimic future conditions adequately and may even be misleading.

Phenyl-Ring-Bearing Cationic Surfactants: Effect of Ring Location on the Micellar Structure

A series of isomeric cationic surfactants (S1-S5) bearing a long alkyl chain that carries a 1,4-phenylene unit and a trimethyl ammonium headgroup was synthesized; the location of the phenyl ring within the alkyl tail was varied in an effort to understand its influence on the amphiphilic properties of the surfactants. The cmc's of the surfactants were estimated using ionic conductivity measurements and isothermal calorimetric titrations (ITC); the values obtained by the two methods were found to be in excellent agreement. The ITC measurements provided additional insight into the various thermodynamic parameters associated with the micellization process. Although all five surfactants have exactly the same molecular formula, their micellar properties were seen to vary dramatically depending on the location of the phenyl ring; the cmc was seen to decrease by almost an order of magnitude when the phenyl ring was moved from the tail end (cmc of S1 is 23 mM) to the headgroup region (cmc of S5 is 3 mM). In all cases, the enthalpy of micellization was negative but the entropy of micellization was positive, suggesting that in all of these systems the formation of micelles is both enthalpically and entropically favored. As expected, the decrease in cmc values upon moving the phenyl ring from the tail end to the headgroup region is accompanied by an increase in the thermodynamic driving force (ΔG) for micellization. To understand further the differences in the micellar structure of these surfactants, small-angle neutron scattering (SANS) measurements were carried out; these measurements reveal that the aggregation number of the micelles increases as the cmc decreases. This increase in the aggregation number is also accompanied by an increase in the asphericity of the micellar aggregate and a decrease in the fractional charge. Geometric packing arguments are presented to account for these changes in aggregation behavior as a function of phenyl ring location.

Denatured-State Conformation As Regulator of Amyloid Assembly Pathways?

Deposits of insoluble protein fibrils with cross beta-sheet structure are the hallmark feature of numerous human disorders, including Alzheimer's disease and type II diabetes. Using correlated dynamic light scattering (DLS) and atomic force microscopy (AFM) we investigated amyloid formation with hen egg white lysozyme at acidic pH values. We found that there was a pronounced transition in the aggregation behavior at low vs near physiological salt concentrations. At low salt concentrations (< 100 mM), DLS indicated the near simultaneous nucleation of three distinct aggregate populations. For elevated salt concentrations, only a single aggregate peak nucleated. AFM imaging shortly after nucleation further indicated distinct aggregate morphologies and sizes. Low salt concentrations yielded polymeric aggregates of varying dimensions but consistent with the three aggregate peaks observed in DLS. Aggregation near physiological salt concentrations, in contrast, yielded oligomeric intermediates that nucleated into protofibril strands. It is commonly accepted that amyloid fibril growth by native proteins requires a partially denatured conformation. We wondered, however, whether these changes in aggregation behavior could be related to differences in the conformation of denatured lysozyme monomers. Using DLS to measure lysozyme's diffusivity, we found that lysozyme assumes a noticeably more extended conformation at low vs. high salt concentrations. These latter measurements were carefully corrected for the effects of protein interaction and variable solution viscosity on protein diffusivity. ANS fluorescence measurements revealed a similar trend towards increased solution exposure of lysozyme monomers at low salt concentrations compared to high salt concentrations. These observations suggest that amyloid fibril assembly pathways might depend on the conformation of the denatured state from which they grow. This has potentially significant implications for our understanding of amyloid fibril formation in general and how to control the emergence of toxic intermediates, in particular.

Pathogenic missense MAPT mutations differentially modulate tau aggregation propensity at nucleation and extension steps

Mutations in the MAPT gene encoding tau protein lead to neurofibrillary lesion formation, neurodegeneration, and cognitive decline associated with frontotemporal lobar degeneration. While some pathogenic mutations affect MAPT introns, resulting in abnormal splicing patterns, the majority occur in the tau coding sequence leading to single amino acid changes in tau primary structure. Depending on their location within the polypeptide chain, tau missense mutations have been reported to augment aggregation propensity. To determine the mechanisms underlying mutation-associated changes in aggregation behavior, the fibrillization of recombinant pathogenic mutants R5L, G272V, P301L, V337M, and R406W prepared in a full-length four-repeat human tau background was examined in vitro as a function of time and submicromolar tau concentrations using electron microscopy assay methods. Kinetic constants for nucleation and extension phases of aggregation were then estimated by direct measurement and mathematical simulation. Results indicated that the mutants differ from each other and from wild-type tau in their aggregation propensity. G272V and P301L mutations increased the rates of both filament nucleation and extension reactions, whereas R5L and V337M increased only the nucleation phase. R406W did not differ from wild-type in any kinetic parameter. The results show that missense mutations can directly promote tau filament formation at different stages of the aggregation pathway.

Reversible aggregation of gold nanoparticles induced by pH dependent conformational transitions of a self-assembled polypeptide

Controlling the stable structures of metallic nanoparticles on mesoscopic and macroscopic length scales is of great interest in nanotechnology. Here, this task is accomplished using a synthetic biopolymer that is responsive to external stimuli and undergoes changes in secondary structure. Reversible aggregation of gold nanoparticles (GNP) is induced by pH dependent changes in a self-assembled monolayer of disulfide modified poly( l-glutamic acid) (SSPLGA) with M w ∼ 27000 . The disulfide anchoring group drives chemisorption onto the gold nanoparticles and leads to the formation of a self-assembled monolayer. Characterization of the modified GNP and its aggregation behavior is performed using dynamic light scattering (DLS), UV–vis and IR spectroscopy, and transmission electron microscopy (TEM). Experimental results show that decrease in pH near 5.5 leads to aggregation of the modified GNP. The change in aggregation behavior with pH occurs within minutes, is reversible, and happens within a narrow range of pH from about 4.5 to 5.5. Comparison with literature data on molar enthalpy of hydrogen bonding, specific optical rotation, and ionization for the helix–coil transition of PLGA indicates that the aggregation of the SSPLGA modified GNP corresponds to the transition in the secondary structure of the polyacid.

The Effects of pH and Ionic Strength on the Aggregation of Bacteriochlorophyll c in Aqueous Organic Media: The Possibility of Two Kinds of Aggregates

AbstractThe aggregation behavior of two homologs of bacteriochlorophyll c (BChl c) in various media was investigated for the effects of pH and salt, and the corresponding structures were analyzed by Fourier transform (FT)‐IR spectroscopy. R‐[P, E] BChl cF (31‐R‐form of BChl c with a propyl group at the C‐8 position and an ethyl group at the C‐12 position) and R‐[E, E] BChl cF (31‐R‐form of BChl c with two ethyl groups at positions C‐8 and C‐12) were isolated from the green sulfur bacterium Chloro‐bium limicola. Aggregates of each homolog showed a pH‐dependent shift of the absorption maximum; at low pH, the peak moved to the red. This tendency was also revealed by circular dichroic spectra. A similar red shift of the peak was also induced by a high concentration of salt (NaCl) or buffer for both homologs. The FT‐IR spectrum indicates that at low pH, both homologs formed a rather amorphous aggregate. On the other hand, a regular structure of R‐[P, E] BChl cF was indicated in an acetone‐water mixture. This structure was stabilized by a triangular interaction among three pigment molecules through the Mg‐OH (3&gt;) O = C (131) linkage. This structure was not found for R‐[E, E] BChl cF. These results indicate that the replacement of the side chain at the C‐8 position on the macrocycle induces a change in aggregation behavior. A possible heterogeneity of the in vivo rod structure of chlorosomes in green sulfur bacteria is discussed based on the above results.

The Effects of pH and Ionic Strength on the Aggregation of Bacteriochlorophyll c in Aqueous Organic Media: The Possibility of Two Kinds of Aggregates

The aggregation behavior of two homologs of bacteriochlorophyll c (BChl c) in various media was investigated for the effects of pH and salt, and the corresponding structures were analyzed by Fourier transform (FT)-IR spectroscopy. R-[P, E] BChl cF (31-R-form of BChl c with a propyl group at the C-8 position and an ethyl group at the C-12 position) and R-[E, E] BChl cF (31-R-form of BChl c with two ethyl groups at positions C-8 and C-12) were isolated from the green sulfur bacterium Chloro-bium limicola. Aggregates of each homolog showed a pH-dependent shift of the absorption maximum; at low pH, the peak moved to the red. This tendency was also revealed by circular dichroic spectra. A similar red shift of the peak was also induced by a high concentration of salt (NaCl) or buffer for both homologs. The FT-IR spectrum indicates that at low pH, both homologs formed a rather amorphous aggregate. On the other hand, a regular structure of R-[P, E] BChl cF was indicated in an acetone-water mixture. This structure was stabilized by a triangular interaction among three pigment molecules through the Mg-OH (3>) O = C (131) linkage. This structure was not found for R-[E, E] BChl cF. These results indicate that the replacement of the side chain at the C-8 position on the macrocycle induces a change in aggregation behavior. A possible heterogeneity of the in vivo rod structure of chlorosomes in green sulfur bacteria is discussed based on the above results.

Effect of Solubilization of Aliphatic Hydrocarbons on Size and Shape of Rodlike C16TABr Micelles Studied by 2H NMR Relaxation

Multifield 2H relaxation has been used to quantify the effect of solubilization of alkanes on the size and shape of the micelles in aqueous solutions of hexadecyltrimethylammonium bromide, C16TABr. Information about aggregate size and shape was deduced from the reorientation rate of the aggregates. The surfactant concentration was chosen so that the solutions without solubilizate contained moderately long rodlike micelles (axial ratio ∼4). It was found that the change in aggregation behavior upon solubilization is substantially different for solubilizates of similar chemical composition but different structures. Solubilization of small amounts of cyclohexane, cyclooctane, cyclodecane, trans-decalin, n-hexane, 2,3-dimethylbutane, or adamantane causes growth of the micelles. Further addition of these solubilizates (except for adamantane, which has a lower solubility limit than the other solubilizates) causes a decrease in the aggregate size. On the other hand, solubilization of n-octane, n-decane, or n-dode...