Aggregation-induced folding of a de novo designed polypeptide immobilized on gold nanoparticles

This communication reports the first steps in the construction of a novel, nanoparticle-based hybrid material for biomimetic and biosensor applications. Gold nanoparticles were modified with synthetic polypeptides to enable control of the particle aggregation state in a switchable manner, and particle aggregation was, in turn, found to induce folding of the immobilized peptides.     

Dynamic covalent polypeptides showing tunable secondary structures and thermoresponsiveness

Lysine‐based polypeptides can be afforded with steerable secondary structures and tunable thermoresponsiveness through dynamic covalent OEGylation. These polypeptides were formed through dynamic imine linkage via reactions of amino moieties from poly(l ‐lysine)s with aldehydes from oligoethylene glycol (OEG)‐based dendrons. In addition to solution concentrations and pH values, macromolecular effect was found to play an important role on the imine formation. OEGylated polypeptides showed characteristic thermoresponsive properties, and their phase transition temperatures were governed predominately by terminal groups and the coverage of OEG dendrons. Notably, thermally induced aggregation would enhance the imine formation even at elevated temperature. In contrast to the covalent polypeptide representatives, the dynamic covalent polypeptides conveyed different thermoresponsiveness due to imine linkages, and their phase transition temperatures could be tuned simply by varying ratios of OEG dendrons with different hydrophilicity. Furthermore, helical conformation of these polypeptides was enhanced with attachment of OEG dendrons, and could be reversibly switched through thermally induced aggregation. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 33–41     

On the extended beta-conformation propensity of polypeptides at high temperature

At room temperature, natural polypeptides exposed to high concentrations of a strong denaturant nearly attain the circular dichroism spectra characteristic of random coils. As temperature is increased, the spectra begin to show the signature of a substantial fraction of extended chain, the structure common in beta-sheets. This structural propensity at high temperature is not altered by concentration changes over a greater than 1000-fold range, so it is not caused by aggregation. Four proteins with different folds and varying amounts of alpha-helical and beta-sheet secondary structure, in the presence or absence of denaturant, all were subject to extended chain formation upon heating. This effect arises naturally from the steric constraints associated with polypeptides and is probably counteracted, not enhanced, by hydrophobic interactions. Molecular dynamics simulations in the 298-1000 K range reveal an attractive potential of mean force in the extended chain region of the Ramachandran diagram, which broadens as the temperature is raised. We also demonstrate a direct correlation between extended structure content and the rate of aggregation kinetics. Thus pre-existing extended structure could funnel proteins into aggregates.     

Small molecule fluorescent probes for the detection of amyloid self-assembly in vitro and in vivo

The misfolding and aggregation of amyloidogenic polypeptides are characteristics of many neurodegenerative syndromes including Alzheimer's and Parkinson's disease. There is a major interest in the availability of amyloid-specific probes that exhibit fluorescence properties, for its use as reporters of protein aggregation in spectroscopy and microscopy methodologies. In this review, we intend to provide an overview of novel fluorescence-based probes and procedures applied for addressing fundamental aspects of amyloid self-assembly in vitro and in vivo. We highlight the utilization in vitro of several small-molecule fluorescent probes as extrinsic and site-specific reporters of amyloid formation, including single-molecule determinations. Detection of amyloid self-assembly employing compounds such as JC-1, DCVJ, ANS derivatives and luminescent conjugated polymers, as well as site-specific probes such as pyrene and ESIPT is discussed. We further review novel fluorescent probes developed for the non-invasive optical imaging of protein aggregates in vivo, including BTA-1, Methoxy-X04, NIAD-4 and CRANAD-2. Availability of increasingly versatile amyloid-specific fluorescent probes is having a very positive impact in the drug discovery and diagnostics fields.     

The influence of different reclamation agents and microorganisms on the aggregative stability of the colloidal fraction of meadow chernozem soil

The influence of various reclamation agents (montmorillonite, peat, activated sludge microbocenosis) on the stability of dispersions of the colloidal fraction of meadow chernozem soil is studied. It is established that biocolloids possess the strongest coagulating action in the aforementioned series of reclamation agents. It is shown that, in the process of microorganism growth involving glucose or polypeptides as a carbon source, exopolymers are synthesized that caused the coagulation of soil dispersions. Upon the growth of microorganisms on polypeptides (alkaligeneous metabolism), precipitates are formed that are denser and less peptized by water than those grown on glucose (acidogeneous metabolism). The addition of montmorillonite and peat intensifies the aggregation processes in soil-microbe heterodispersions. The inverse relationship between the content of an organic substance in a colloidal system and the stability of aggregates of soil colloids is revealed.     

Self-assembly of amylin(20-29) amide-bond derivatives into helical ribbons and peptide nanotubes rather than fibrils

Uncontrolled aggregation of proteins or polypeptides can be detrimental for normal cellular processes in healthy organisms. Proteins or polypeptides that form these amyloid deposits differ in their primary sequence but share a common structural motif: the (anti)parallel beta sheet. A well-accepted approach for interfering with beta-sheet formation is the design of soluble beta-sheet peptides to disrupt the hydrogen-bonding network; this ultimately leads to the disassembly of the aggregates or fibrils. Here, we describe the synthesis, spectroscopic analysis, and aggregation behavior, imaged by electron microscopy, of several backbone-modified amylin(20-29) derivatives. It was found that these amylin derivatives were not able to form fibrils and to some extent were able to inhibit fibril growth of native amylin(20-29). However, two of the amylin peptides were able to form large supramolecular assemblies, like helical ribbons and peptide nanotubes, in which beta-sheet formation was clearly absent. This was quite unexpected since these peptides have been designed as soluble beta-sheet breakers for disrupting the characteristic hydrogen-bonding network of (anti)parallel beta sheets. The increased hydrophobicity and the presence of essential amino acid side chains in the newly designed amylin(20-29) derivatives were found to be the driving force for self-assembly into helical ribbons and peptide nanotubes. This example of controlled and desired peptide aggregation may be a strong impetus for research on bionanomaterials in which special shapes and assemblies are the focus of interest.     

Vibrational circular dichroism study of solvent- and temperature-induced conformational changes in poly-γ-benzyl-l-glutamate and poly-β-benzyl-l-aspartate

Vibrational circular dichroism (VCD) spectroscopy was used to study the effect of the different composition of mixed solvents and temperature on the conformation and aggregation states of two synthetically prepared polypeptides, poly-γ-benzyl-l-glutamate (PBLG) and poly-β-benzyl-l-aspartate (PBLA).Additions of trifluoroacetic acid (TFA) into a solution of heligenic solvents trichloromethane and benzene-d6 caused the conformational change from the α-helical to polyproline II-like for both of the polypeptides, which represented interesting transition previously mostly observed in aqueous solutions rather than in organic solvents. The VCD method proved a lower stability of the α-helical conformation of PBLA than PBLG and the structural differences between these polypeptides.The variation of temperature in the region 13–50 °C induced atypical conformational transformations in the PBLG/trichloromethane/TFA and PBLG/benzene-d6/TFA systems. The usually more stable α-helical conformation was observed at higher temperatures than the polyproline II-like conformation.     

Understanding self-assembly of rod-coil copolymer in nanoslits

Rod-coil diblock copolymers are a special kind of molecule containing a rigid rod and a flexible part. We present a systematic study on self-assembly of the rod-coil copolymers in nanoslits using a hybrid density functional theory. The self-assembly of the rod-coil molecule is driven by the bulk concentration, and there exists a critical bulk concentration beyond which the rod-coil molecule self-assembled into ordered lamellar structures in the slit, otherwise it is in a disordered state. By monitoring the effect of the interaction (epsilon(TT)(*)) of molecular tail on the self-assembly, we found that in the nanoslit of H=13sigma, it is at epsilon(TT)(*)=8 rather than epsilon(TT)(*)=10 or epsilon(TT)(*)=12 that the minimal critical bulk concentration occurs. It may be because the strong tail-tail interaction leads to aggregation of the copolymer molecules in bulk phase, and the resulting supramolecular structures are fairly difficult to enter the slit due to the depletion effect. At a fixed slit, the structural evolution of the self-assembled film with the bulk concentration is observed, including trilayer and five-layer lamellar structures, smectic-A, smectic-C, and a mixture of smectic-A and smectic-C liquid crystal phases and so on. We found that the critical bulk concentration, corresponding to the disordered-ordered phase transition, greatly depends on the separation between two walls, and it changes periodically with the increase of the slit width. In addition, it is also found that the molecular flexibility is one of key factors determining the self-assembled structure in the slit, and the critical bulk density increases with the molecular flexibility.     

Spin-label study of the conformational states of polypeptide models of histones

The conformational states of the regular polypeptides (Gly-Lys-Gly)_n, (Ala-Orn-Gly)_n, and (Ala-Orn-Ala)_n have been studied by the spin-label method. Their behavior in solutions of guanidine hydrochloride and urea and in solutions of salts of bivalent metals does not contradict the presence of an extended levohelical conformation in their polypeptide chains. In CaCl₂ (5 N) solutions the polypeptides exhibit aggregation properties. A study of the behavior of the poly peptide at these temperatures has shown that with a rise in temperature there is a monotonic change in the structures of the polypeptide chains that is characteristic for a conformation of the polyproline-II type. Differences have been observed in the behavior of glycine-and alanine-containing polypeptides in the presence of sodium dodecyl sulfate with a change in the temperature.V. I. Nikitin Institute of Chemistry of the Academy of Sciences of the Tadzhik SSR, Dushanbe. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 218–222, March–April, 1986.     

Chiral interaction of sequential lysine polypeptides with methyl orange. Effects of distance between lysine residues and hydrophobic side chains

Two series of sequential poly(Lys-X) (X: Gly, Ala, and Ahx in series A; Gly, Ala, Leu and Phe in series B) have been synthesized. On the chiral interaction between cationic polypeptides and methyl orange (MO), the effects of the distance (series A) and of the hydrophobic side chains (series B) were examined by means of the absorption and induced circular dichroism (CD) spectroscopies. Dichroic bands associated with the blue shifted absorption peaks or shoulders of MO in the visible wavelength region were observed by complex formation between the polypeptides and the dye. The intensity of the induced CD was affected by the concentration of the complexes and time after preparing the complex solutions, suggesting the formation of the intermolecular aggregation in some instances. When MO molecules bound to lysine residues are apart from each other, the aggregation of the complexes is not marked. Roughly, the intensity of the induced CD decreases with increasing distance between the intramolecular lysine residues in series A polypeptides. When the hydrophobicity of the side chains is increased, the induced CD spectra of the series B polypeptide-MO complexes exhibits the inversion of the sign of the induced CD extrema.     

New Conjugated Molecules with Two and Three Dithienyldiketopyrrolopyrrole (DPP) Moieties Substituted at meta Positions of Benzene toward p‐ and n‐Type Organic Photovoltaic Materials

Two conjugated molecules, TADPP3 and TADPP2‐TT , are reported, in which three and two dithienyldiketopyrrolopyrrole (DPP) moieties, respectively, are substituted at the meta positions of benzene. Based on cyclic voltammetry and absorption data, TADPP3 and TADPP2‐TT possess similar HOMO and LUMO energies of about ?5.2 and ?3.4 eV, respectively. Thin films of TADPP3 and TADPP2‐TT exhibit p‐type semiconducting behavior with hole mobilities of 2.36×10^?3 and 3.76×10^?4 cm² V^?1 s^?1 after thermal annealing. Molecules TADPP3 and TADPP2‐TT were utilized as p‐type photovoltaic materials to fabricate organic solar cells after blending with phenyl C₇₁ butyric acid methyl ester ( PC₇₁BM ) and phenyl C₆₁ butyric acid methyl ester ( PC₆₁BM ). The relatively low J_SC and fill factor values can be attributed to poor film morphologies based on AFM and XRD studies. A solar cell with a thin film of TADPP3 with PC₇₁BM in a weight ratio of 1:2 exhibits a high open‐circuit voltage (V_OC) of 0.99 V and a power conversion efficiency (PCE) of 2.47 %. Interestingly, TADPP3 can also be employed as an n‐type photovoltaic material. The blended thin film of TADPP3 with P3HT in a weight ratio of 1:2 gave a high V_OC of 1.11 V and a PCE of 1.08 % after thermal annealing.     

An Intracellular H2O2‐Responsive AIEgen for the Peroxidase‐Mediated Selective Imaging and Inhibition of Inflammatory Cells

Inflammatory cells have gained widespread attention because inflammatory diseases increase the risk for many types of cancer. Therefore, it is urgent and important to implement detection and treatment methods for inflammatory cells. Herein, we constructed a theranostic probe with aggregation‐induced emission (AIE) characteristics, in which tetraphenylethene (TPE) was modified with two tyrosine (Tyr) moieties. Owing to the H₂O₂‐dependent, enzyme‐catalyzed dityrosine formation, Tyr‐containing TPE ( TT ) molecules crosslink through dityrosine linkages to induce the formation of hydrophobic aggregates, activating the AIE process in inflammatory cells that contain H₂O₂ and overexpress myeloperoxidase. The emission turn‐on resulting from the crosslinking of TT molecules could be used to distinguish between inflammatory and normal cells. Moreover, the massive TT aggregates induced mitochondria damage and cell apoptosis. This study demonstrates that the H₂O₂‐responsive peroxidase‐activated AIEgen holds great promise for inflammatory‐cell selective imaging and inhibition.     

Morphology and phase separation of hydrophobic clusters of soy globular protein polymers

Protein hydrophobic interaction has been considered the most important factor dominating protein folding, aggregation, gelling, self-assembly, adhesion, and cohesion properties. In this paper, morphology and phase separation of hydrophobic clusters, networks, and aggregates of soy globular protein polymers, induced by using a reducing agent (NaHSO3), are studied using microscopic instruments. The morphology and phase separation of these hydrophobic clusters are sensitive to protein structure and composition, pH, and ionic-strength (I(m)). Most of the clusters are in spherical-shape architecture and mainly consist of hydrophobic polypeptides. Rod-shape clusters were also observed at higher ionic strength, and mainly consist of hydrophilic polypeptides. The ratio of hydrophobic/hydrophilic (HB/HL) polypeptides is important to facilitate the formation of clusters in an environment with a certain pH value and ionic strength. At HB/HL 0.8, uniform spherical clusters were observed and diameters ranged from 30 to 70 nm. At HB/HL <0.8, large spherical clusters were formed with diameters ranging from 100 to 1,000 nm, and at HB/HL >or=1.8, large hydrophobic aggregates formed, and size of aggregates can be up to 2 500 nm. When solid content increased from 3% to 38%, at I(m) or= 0.115 mol x L(-1), HB/HL ratio >or=1.8, the large aggregates became very cohesive and viscoelastic. Clear phase separation was observed during curing between hydrophobic and hydrophilic protein polymers. Phase-separation degree increased as HB/HL ratio increased.     

Effects of alkyl side chain length of low bandgap naphtho[1,2‐c:5,6‐c′]bis[1,2,5]thiadiazole‐based copolymers on the optoelectronic properties of polymer solar cells

Two donor‐π‐acceptor (D‐π‐A) type naphtho[1,2‐c:5,6‐c′]bis[1,2,5]thiadiazole (NT)‐based conjugated copolymers (CPs), namely, PBDT‐TT‐DTNT‐HD and PBDT‐TT‐DTNT‐OD, containing different side chain length (2‐hexyldecyl, HD and 2‐octyldodecyl, OD) anchoring to thiophene π‐bridge between the two‐dimensional (2D) 5‐((2‐butyloctyl)thieno[3,2‐b]thiophen‐2‐yl)benzo[1,2‐b:4,5‐b′]dithiophene (BDT‐TT) unit and NT moiety are developed and fully characterized. The resultant two copolymers exhibited broader absorption in wide range of 300–820 nm and obviously deepened E_HOMO of approximately −5.50 eV. The effects of side chain length on film‐forming ability, absorption, energy levels, aggregation, dielectric constant (ɛ_r), mobility, morphology, and photovoltaic properties are further systematically investigated. It was found that the side chain length had little impact on solution‐processability, absorption, energy levels, and aggregation in CB solution of resultant CPs. However, tinily increasing side chain length promoted to form the more ordered structure of neat polymer film even if the corresponding ɛ_r decreased. As a result, the side‐chain‐extended PBDT‐TT‐DTNT‐OD:PC₇₁BM‐based device achieved 32% increased FF than that of PBDT‐TT‐DTNT‐HD:PC₇₁BM and thus the PCE was significantly raised from 3.99% to 5.21%, which were benefited from 2 times higher SCLC hole mobility, more favorable phase separation, and improved exciton dissociation. These findings could provide an important and valuable insight by side chain modulation for achieving efficient PSCs. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018 , 56, 2059–2071     

Diketopyrrolopyrrole‐based polymer nanowires: Control of chain conformation and nucleation

Understanding the nucleation process is very important in growing polymer nanowires as it plays a decisive role in determining the crystal structure and size distribution. Polymer chain conformation determines whether the polymer chains could assemble to nuclei or not. Here, chain conformation and the nucleation process were controlled to grow 3,6‐bis‐(thiophen‐2‐yl)‐N,N′‐bis(2‐decyl‐1‐tetradecyl)‐1,4‐dioxo‐pyrrolo[3,4‐c]pyrrole and thieno[3,2‐b]thiophene (DT‐PDBT‐TT) nanowires. We changed the conformation of DT‐PDBT‐TT in solution and controlled the nucleation process by using a main solvent:cosolvent system. The main solvent was a low boiling point good solvent, and the cosolvent was consisted of two high boiling point solvents with different solubility. In fact, the chain conformation in the pristine solution was changed by choosing different main solvents (with H‐bond, π–π or none interaction with the main chain) and temperatures. The absorption spectrum and TEM images showed that trichloro ethylene (TCE) was the best main solvent because it has H‐bond interaction with the polymer main chain and DT‐PDBT‐TT conformation in it approaching unimer coil conformation, which is beneficial to grow nanowires. Mixed o‐dichlorobenzene (ODCB) and anisole (AS) with different ratios were used to changing the solubility step by step to control nucleation process. Only when marginal cosolvent (ODCB:AS = 1:1) was added, could it decrease the nuclei number and avoided the aggregates simultaneously. As the main solvent evaporated slowly, the nucleation and growth happened, leading to the nanowires formation. The resulting nanowires were about 63 nm in width and one to two microns in length. The width of the DT‐PDBT‐TT structures suggests that the polymer chains are oriented along the fibril axis. Our results indicated that there are two requirements for the nanowire formation, (1) the polymer chain conformation should approach unimer coil; (2) the nucleation density should be optimized, not too much and no aggregation happened. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 833–841     

Noncovalent interactions in human plasma proteins analyzed by the comparison of nondenaturing and denaturing micro-2-D gel electrophoresis patterns after polypeptide assignment using matrix-assisted laser desorption/ionization-mass spectrometry and peptide mass fingerprinting

Previously, we reported the analysis of human plasma proteins by 2-DE under nondenaturing conditions (Type-I 2-DE) followed by the assignment of stained spots using MALDI-MS and PMF [1]. Here, we employ 2-DE conditions modified only in the second-dimensional separation; SDS was added in the gradient slab gel aiming to dissociate noncovalently bound proteins/polypeptides (Type-II 2-DE). Totally 169 CBB-stained spots on a micro-2-DE gel were numbered and subjected to polypeptide assignment using MALDI-MS-PMF. One hundred sixty spots out of the 169 provided significant match (p <0.05) with polypeptides in databases. Comparisons of the results of polypeptide assignment on the two 2-DE patterns indicated that 10 polypeptides in 20 stained spots on the Type-I 2-DE pattern [1] shifted toward low-molecular-weight positions on the Type-II 2-DE pattern, demonstrating the presence of noncovalent interactions. Seventeen polypeptides in 38 stained spots were only assigned on the Type-II 2-DE gel, which could mostly be accounted for by the disruption of noncovalent protein-protein interactions in the presence of SDS, i.e., protein/polypeptide complexes which might form smear bands on the Type-I 2-DE gel dissociate to form clear spots on the Type-II 2-DE gel. The method employed here, comparisons of nondenaturing and denaturing 2-DE maps with polypeptide assignment by MALDI-MS-PMF, would enable the simultaneous detection of multiple noncovalent interactions in complex protein/polypeptide systems.     

New Series of Pyrazoles and Imidazo-Pyrazoles Targeting Different Cancer and Inflammation Pathways

(1) Background: different previously synthesized pyrazoles and imidazo-pyrazoles showed interesting anti-angiogenic action, being able to interfere with ERK1/2, AKT and p38MAPK phosphorylation in different manners and with different potency; (2) Methods: here, a new small compound library, endowed with the same differently decorated chemical scaffolds, has been synthetized to obtain new agents able to inhibit different pathways involved in inflammation, cancer and human platelet aggregation. (3) Results: most of the new synthesized derivatives resulted able to block ROS production, platelet aggregation and p38MAPK phosphorylation both in platelets and Human Umbilical Vein Endothelial cells (HUVEC). This paves the way for the development of new agents with anti-angiogenic activity.     

Formation of particles of metal hydroxides in water solution of polymer

The stages of the formation of metal hydroxide particles in water medium were described. The first stage is the formation of complexes between the stabilizer and metal ion or of metal polyions containing a few metal ions. Dependence between the number of metal ions in polyion and its charge on the pH is described. The second stage is the formation of the metal hydroxide particles by the aggregation of polyions or their adsorption on/in the stabilizer. The distribution of the polyion number in the particles in polyion aggregation is described by the equation p(k) = k(ks-1)(k-1)/ksk and in polyion adsorption on/in the stabilizer particles is more narrow and is described by the equation p(k) = exp(-ks)/ks(-k)/k!, where k and ks are the number and the average number of polyions in the particle.     

Taylor dispersion analysis discloses the impairment of Aβ peptide aggregation by the presence of a fluorescent tag

The use of fluorescently tagged amyloid peptides, implicated in Alzheimer's disease, to study their aggregation at low concentrations is a common method; however, the fluorescent tag should not introduce a bias in the aggregation process. In this work, native amyloid peptides Aβ(1–40) and Aβ(1–42) and fluorescein-5-isothiocyanate (FITC), tagged ones, were studied using Taylor dispersion analysis coupled with a simultaneous UV and light-emitting diode-induced fluorescence detection, to unravel the effect of FITC on the aggregation process. For that, a total concentration of 100 µM of peptides consisting of a mixture of native and tagged ones (up to 10% in moles) was applied. Results demonstrated that FITC had a strong inhibition effect upon the aggregation behaviour of Aβ(1–42), whereas for Aβ(1–40), only a retardation in kinetics was observed. It was also shown that when mixed solutions of Aβ(1–40) and Aβ(1–42) are used, the Aβ(1–42) alloform was the leading peptide in the aggregation process, and when the latter was tagged, the aggregation kinetics decreased but the lifetime of potentially toxic oligomers was drastically increased. These results confirmed that the hydrophilicity of the N-terminus part of the peptide plays a major role in the aggregation process.     

Selective Peptide Cysteine Manipulation on Demand and Difficult Protein Chemical Synthesis Enabled by Controllable Acidolysis of N,S-Benzylidene Thioacetals

Although solid-phase peptide synthesis combining with chemical ligation provides a way to build up customized polypeptides in general, many targets are still presenting challenges for the conventional synthetic process, such as hydrophobic proteins. New methods and strategies are still required to overcome these obstacles. In this study, kinetic studies of Cys/Pen ligation and its acidolysis were performed, from which the fast acidolysis of substituted N,S-benzylidene thioacetals (NBTs) was discovered. The study demonstrates the potential of NBTs as a promising Cys switchable protection, facilitating the chemical synthesis of peptides and proteins by efficiently disrupting peptide aggregation. The compatibility of NBTs with other commonly adopted Cys protecting groups and their applications in sequential disulfide bond formation were also investigated. The first chemical synthesis of the native human programmed death ligand 1 immunoglobulin V-like (PD-L1 IgV) domain was achieved using the NBT strategy, showcasing its potential in difficult protein synthesis.