Ionic peptide aggregation: exploration of conformational dynamics in aqueous solution by computational techniques

The effects of end groups on KEK peptide conformational characteristics and self-assembling properties in water solution are investigated by using long lasting all-atom molecular dynamics simulations. The analysis of the structural macroscopic and microscopic properties and the examination of intra- and intermolecular interactions suggest, in agreement with experimental observations, the role played by side chains and terminal regions in determining the characteristic features of the assemblages. Competition between intra- and interchain interactions greatly affects the diffusivity of peptide molecules and the conformational space that they can sample, ultimately controlling the shape, size, and distribution of the aggregate configurations. Different peptide end groups influence peptide flexibility and seem to play a crucial role in determining the aggregates' supramolecular architectures.     

The aggregation of trichosanthin in aqueous solution

As a kind of cytotoxin extracted from the root tuber of Trichosanthes kirilowii Maxim (Cucurbitaceae), trichosanthin can selectively bind to and kill the placental trophoblastic cells, which leads to a number of biomedical applications including the inhibition of trophoblastic tumors. However, the stability of trichosanthin in living organism is still one of the problems hindering the effectiveness of its applications. In this study, laser light scattering has been used successfully to investigate the stability of trichosanthin in both deionized water and KSCN aqueous solution in terms of the hydrodynamic size distribution of the trichosanthin aggregates as a function of both time and the salt concentration. It is found that the size distribution is always a bimodal one. One peak corresponds to a single trichosanthin chain; the other corresponds to the trichosanthin aggregates, which have an average hydrodynamic radius of ∼ 49 nm and are composed of ∼ 127 trichosanthin molecules when C_KSCN is higher than 0.5 mol/L. This implies that there exists an equilibrium between the single trichosanthin chain and its aggregates [i.e., nT ⇄ (T)_n]. Our results also suggest that the aggregates are made of the loosely packed trichosanthin molecules and behave as flexible polymer chains in θ solvent. © 1996 John Wiley & Sons, Inc.     

Effect of the nature of the spacer on the aggregation properties of gemini surfactants in an aqueous solution

The aggregation properties of three dicationic quaternary ammonium gemini surfactants with the same structure, except the spacer group, diethyl ether, six methylene, and p-xylyl, have been studied using electrical conductivity and fluorescence. The critical micelle concentration (cmc) and the micelle aggregation number (N) were determined, and the micropolarity and the microviscosity of the micelle were characterized. The micelle ionization degree (alpha) was obtained by a combination of the electrical conductivity data and the micelle aggregation number. Furthermore, the Gibbs free energy of micellization (deltaGmic) was studied. These results have shown that the nature of the spacer has an important effect on the aggregation properties of gemini surfactants in an aqueous solution. A hydrophilic, flexible spacer prompts micelle formation, which leads to a smaller cmc, smaller alpha, larger N, and more negative deltaGmic. Meanwhile, the microviscosity study indicates that the gemini surfactant with a hydrophilic, flexible spacer forms a more closely packed micelle structure than the one with a hydrophobic, rigid spacer.     

Salt effects on aggregation of O-carboxymethylchitosan in aqueous solution

The effects of salt with different valences (NaCl, CaCl2 and CrCl3) on the aggregation of O-carboxylmethylchitosan (OCMCS) in dilute aqueous solution were investigated using viscometry, dynamic laser light scattering (DLS) and atomic force microscopy (AFM). With increasing OCMCS concentration beyond a critical aggregation concentration (cac) of approximately 0.045 g/l, the aggregation of OCMCS appears in solution. The driving forces of the OCMCS aggregation are intermolecular hydrogen bond, hydrophobic interaction and electrostatic repulsion. The OCMCS aggregation behavior strongly depends on the valence of salt. When NaCl is added, the aggregate size increases with NaCl concentration. When CaCl2 or CrCl3 is added to a given OCMCS concentration, there exists a critical concentration each of Ca2+ and Cr3+. Before the critical concentration, the aggregates decrease in size with increasing salt concentration due to the intra-aggregate complexation; while after the critical concentration, the size of the aggregates increases with salt concentration due to the inter-aggregate complexation. Moreover, the effect of Cr3+ on the OCMCS aggregation is greater than that of Ca2+. The formation of the intra-aggregate complexation is found to be a kinetic process and the aggregate size decreases with time; the formation of the inter-aggregate complexation is also kinetic where the aggregate size increases with time. The aggregates dominated by the intra-aggregate complexation are small, compact and spherical, while the aggregates dominated by the inter-aggregate complexation show the big, compact and spherical morphology.     

Beta-hairpin folding by a model amyloid peptide in solution and at an interface

The development of specific agents against amyloidoses requires an understanding of the conformational distribution of fibrillogenic peptides at a microscopic level. Here, I present molecular dynamics simulations of the model amyloid peptide LSFD with sequence LSFDNSGAITIG-NH2 in explicit water and at a water/vapor interface for a total time scale of approximately 1.8 micros. An extended structure was used as initial peptide configuration. At approximately 290 K, solvated LSFD was kinetically trapped in diverse misfolded beta-sheet/coil conformations. At 350 K, in contrast, the same type II' beta-hairpin in equilibrium with less ordered but also U-shaped conformations was observed for the core residues DNSGAITI in solution and at the interface in multiple independent simulations. The most stable structural unit of the beta-hairpin was the two residue turn (GA). The core residues exhibited a well-defined folded state in which the beta-hairpin was stabilized by a hydrogen bond between the side chain of Asn-385 and the main chain carbonyl group of Gly-387. My results suggest that beta-sheet conformations indicated from previous Fourier-transform infrared spectroscopy measurements immediately after preparation of the peptide solution may not arise from protofilaments as speculated by others but are a property of LSFD monomers. In addition, combined with previous results from X-ray scattering, my findings suggest that interfacial aggregation of LSFD implies a transition from U-shaped to extended peptide conformations. This work including the first simulations of reversible beta-hairpin folding at an interface is an essential step toward a microscopic understanding of interfacial peptide folding and self-assembly. Knowledge of the main conformation of the peptide core may facilitate the design of possible inhibitors of LSFD aggregation as a test ground for future computational therapeutic strategies against amyloid diseases.     

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the beta-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides     

A self-diffusion study in aqueous solution and lyotropic mesophases of amphiphilic block copolymers

 Water-soluble poly(ethylene oxide)–poly(propylene oxide)–poly(ethylene oxide) (PEO–PPO–PPO) triblock copolymers are high-molecular-weight nonionic copolymers and form micellar solutions and liquid-crystalline mesophases in water. We studied the temperature dependence of polymer and water self-diffusion in solutions and lyotropic mesophases of the PEO₁₃ PPO₃₀ PEO₁₃/water and PEO₂₁ PPO₄₇ PEO₂₁/water binary systems. The self-diffusion measurements were performed by means of the pulsed field gradient spin-echo NMR method. The analysis of the water mobility was realised using “the obstruction factor” and “the two-site model”, which consider the reduction of the water self-diffusion due to the microstructure of the lyotropic aggregates and to the presence of one part of the solvent bound to the polymer aggregate surfaces. We calculated the water obstruction factors and the hydration numbers as a function both of the polymer composition and of the temperature. The results are compared with the data obtained in mesophases formed by classical surfactants. Received: 16 September 1999 Accepted in revised form: 24 November 1999     

Effect of phenol on the aggregation characteristics of an ethylene oxide-propylene oxide triblock copolymer P65 in aqueous solution

The effects of phenol on the micellization, micellar growth, and phase separation of a poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-PPO-PEO) amphiphilic copolymer (Pluronic P65: EO19 PO30 EO19) in aqueous solution have been studied by cloud point, viscosity, dynamic light scattering (DLS), differential scanning calorimetry (DSC), fluorescence spectroscopy, and small-angle neutron scattering (SANS). Various concentrations of P65 have been chosen to estimate the effect of phenol on different concentration regions of P65. Phenol interacts quite differently at low concentrations (0-2%) than at high concentrations (2-10%) of P65, as per the observation that phenol is more predominant at smaller concentrations of P65. A marked decrease in the cloud points of the P65 solutions is observed in presence of phenol. The critical micelle temperature (CMT) of P65 shows a synergistic effect of phenol on P65 aggregates. Micellar transitions, phase separation, and aggregation behaviours like micellization and micellar growth in the presence of phenol have been observed by combining viscometry, DLS, DSC, and CP. DLS shows that the effect of phenol is predominant at high temperatures. SANS shows a high increase in axial ratio and aggregation numbers in the presence of phenol at fixed concentrations of P65. Fluorescence data illustrate that addition of phenol makes micelles polar but at the same time its favours aggregation. Water-soluble phenol (present in low concentrations) forms aggregates with P65, which can be separated by cloud point extraction, making this study interesting for separation of phenol from the phenol-water system.     

Oil-induced aggregation of block copolymer in aqueous solution

The oil-induced aggregation behavior of PEO-PPO-PEO Pluronic P84 [(EO)19(PO)39(EO)19] in aqueous solutions has been systematically investigated by 1H NMR spectroscopy, freeze-fracture transmission electron microscopy (FF-TEM), and dynamic light scattering (DLS). The critical micellization temperature (CMT) for P84 in the presence of oils decreases with increasing oil concentration. The effectiveness of various oils in decreasing the CMT of block copolymer follows the order m-xylene (C(8)H(10)) > toluene (C(7)H(8)) > benzene (C(6)H(6)) > n-octane (C(8)H(18)) > n-hexane (C(6)H(14)) approximately cyclohexane (C(6)H(12)). It was found that the amount of anhydrous PO methyl groups increases whereas the amount of hydrated PO methyl groups decreases upon the addition of oils. At low oil concentration, the oil molecules are entrapped by the micellar core, but as the oil concentration increases above a certain value, the micellar core swells significantly as a result of the penetrated oil molecules, and much larger aggregates are formed. Intermolecular rotating-frame nuclear Overhauser effect (ROE) measurements between P84 and benzene were performed at 10 and 40 degrees C. The specific interaction between benzene and the methyl groups of PPO was determined, and it was observed that the interaction site remained unchanged as the temperature was increased.     

Effect of hydrophobic chains on the aggregation behavior of cationic silicone surfactants in aqueous solution

Three cationic silicone surfactants, (2-hydroxyethyl)-N,N-dimethyl-3-[tri-(trimethylsiloxy)]silylpropylammonium chloride (Si₄ACl), (2-hydroxyethyl)-N,N-dimethyl-3-[bis(trimethylsiloxy)methyl]silylpropylammonium chloride (Si₃ACl), and (2-hydroxyethyl)-N,N-dimethyl-3-[bis(trimethylsilylmethyl)methyl]silylpropyl-ammonium chloride (Si₃C₂ACl), with the same headgroups and different hydrophobic groups were synthesized. Their aggregation behavior in aqueous solution was investigated by surface tension and electrical conductivity. The results show that all the three cationic silicone surfactants perform admirable surface activity. Because of the effect of the hydrophobic groups, the critical micelle concentration values increase following the order Si₃C₂ACl?<?Si₄ACl?<?Si₃ACl, and Si₃C₂ACl packs more compactly at the air/water interface compared with Si₄ACl and Si₃ACl. Electrical conductivity studies show that all the three cationic silicone surfactants have low degree of counterion binding. Thermodynamic parameters ( $ \varDelta\;H_m^0 $ , $ \varDelta S_m^0 $ , and $ \varDelta G_m^0 $ ) of micellization derived from electrical conductivities indicate that the micellization for both Si₃C₂AC and Si₃ACl in aqueous solution is enthalpy-driven, and that for the Si₄ACl is entropy-driven. For the heat capacities, $ \varDelta\;c_{m,p}^0 $ , values are positive for Si₄ACl, indicating that there is an attractive interaction between the nitrogen atom of one surfactant molecule and the oxygen atom of another surfactant molecule for Si₄ACl.     

Effect of ionic liquids on the aggregation behavior of PEO-PPO-PEO block copolymers in aqueous solution

Effect of 1-butyl-3-methyl-imidazolium bromide (BmimBr) on the aggregation behavior of PEO-PPO-PEO Pluronic P104 aqueous solution was studied by Fourier transform infrared (FTIR) spectroscopy, freeze fracture transmission electron microscopy (FF-TEM), dynamic light scattering (DLS), and NMR spectroscopy. When the BmimBr concentration was below 1.232 mol/L, the critical micelle temperature (CMT) of Pluronic P104 remained constant, while the size of micelles increased with increasing the BmimBr concentration; above this concentration, the CMT of Pluronic P104 decreased abruptly, and bigger clusters of BmimBr were formed. The selective nuclear Overhauser effect (NOE) spectrum indicates that the PO block of the P104 interacts with the butyl group of the Bmim+ cation by hydrophobic interaction. It suggests that when the concentration of BmimBr is below 1.232 mol/L, there are P104 micelles in the aqueous solution with BmimBr embedding to the micellar core, while above this concentration, P104 micelles and BmimBr clusters coexist in the system.     

Substrate binding to cyclodextrins in aqueous solution: A multicomponent self-diffusion study

It is demonstrated that substrate binding to α- and β-cyclodextrins (CD) in solution can conveniently and directly be monitored from multicomponent self-diffusion data on these solutions, using the Fourier Transform NMR pulsed-gradient spin-echo technique. Included are aromatics and a series of alcohols ranging from methanol to octanol. Experimentally it was found thatn-alcohols associate more strongly with α-CD than with β-CD. As the bulkiness of the alcohol increased, binding to β-CD was enhanced while the reverse effect was observed in the case of α-CD. For both cyclodextrins it was found thatn-alcohol complexation in the homologous series was attributable to an increment in standard free energy of complexation of ～ ?3.0 kJ/mol for each ?CH₂? group, suggesting that the binding mechanism is of a hydrophobic nature.     

Effects of the thermal history and concentration on the aggregation of Erwinia gum in an aqueous solution

The aggregation of Erwinia (E) gum in a 0.2 M NaCl aqueous solution was investigated by multi‐angle laser light scattering and gel permeation chromatography (GPC) combined with light scattering. The GPC chromatograms of five fractions contained two peaks; the fractions had the same elution volume but different peak areas, suggesting that aggregates and single chains coexisted in the solution at 25 °C. The apparent weight‐average molecular weights (M_w) of the aggregates and single chains for each fraction were all about 2.1 × 10⁶ and 7.8 × 10⁴, respectively. This indicates that the aggregates were composed of about 27 molecules of E gum in the concentration range used (1.0 × 10⁻⁶ to 5.0 × 10⁻⁴ g/mL). The weight fraction of the aggregates (w_ag) increased with increasing concentration, but the aggregates still existed even in an extremely dilute solution. The fractionation process and polymer concentration hardly affected the apparent aggregation number but significantly changed w_ag. The E‐gum M_w decreased sharply with an increase in temperature. When the E‐gum solution was kept at 100 °C, w_ag decreased sharply for 20 h and leveled off after 100 h. Once the aggregates were decomposed at a higher temperature, no aggregation was observed in the solution at 25 °C, indicating that the aggregation was irreversible. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1352–1358, 2000     

The aggregation behavior of O-carboxymethylchitosan in dilute aqueous solution

O-Carboxymethylchitosan (OCMCS) is a kind of biocompatible derivatives of chitosan whose water solubility is strongly dependent on the degree of carboxymethylation. The OCMCS with 100 carboxymethyl groups and 75 amino groups per 100 anhydroglucosamine units of OCMCS was synthesized by the reaction of chitosan and monochloroacetic. When OCMCS was dissolved in water, its solution was neutral and OCMCS behaved like a weak polyanionic polyeclectrolyte because most of carboxylic groups were not dissociated in neutral aqueous solution. The aggregation behavior of OCMCS in aqueous solution was studied by surface tensiometry, steady-state fluorescence spectroscopy and viscometry. The critical aggregation concentration (cac) of OCMCS was determined to be between 0.042 mg/ml and 0.050 mg/ml. The possible aggregation mechanism of OCMCS in water was elucidated.     

Temperature effects on the aggregation of decylpyridinium chloride in aqueous solution

Surface tension and conductivity measurements were used to study micelle formation in an aqueous solution of decylpyridinium chloride at 20, 25, 30, 35, and 40°C. The critical micelle concentration (CMC) was minimum at about 30–35°C. After CMC₁, aggregation with CMC₂ and CMC₃ occurred as the concentration increased.     

Wetting and freezing of hexadecane on an aqueous surfactant solution: triple point in a 2-D film

Wetting of water by hexadecane has been investigated by ellipsometry as a function of the concentration of the cationic surfactant dodecyltrimethylammonium bromide (DTAB) in the aqueous phase and temperature. Three phases are identified: a 2-D gas of hexadecane molecules and DTAB molecules, a 2-D liquid comprising a mixed monolayer of hexadecane and DTAB, and a 2-D 'solid' phase. Evidence is presented to support the hypothesis that the liquid-solid phase transition is actually a wetting transition in which a surface-frozen layer of pure hexadecane wets the liquid-like mixed monolayer of hexadecane and DTAB. The triple point, at which the three phases coexist, is located at a temperature of 17.3 degrees C and DTAB concentration of 0.75 mmol kg (-1). The slopes of the three phase boundaries are analyzed thermodynamically.     

Formation and stability of peptide enolates in aqueous solution

Second-order rate constants k(DO) (M(-1) s(-1)) were determined in D(2)O for deprotonation of the N-terminal alpha-amino carbon of glycylglycine and glycylglycylglycine zwitterions, the internal alpha-amino carbon of the glycylglycylglycine anion, and the acetyl methyl group and the alpha-amino carbon of the N-acetylglycine anion and N-acetylglycinamide by deuterioxide ion. The data were used to estimate values of k(HO) (M(-1) s(-1)) for proton transfer from these carbon acids to hydroxide ion in H(2)O. Values of the pK(a) for these carbon acids ranging from 23.9 to 30.8 were obtained by interpolation or extrapolation of good linear correlations between log k(HO) and carbon acid pK(a) established in earlier work for deprotonation of related neutral and cationic alpha-carbonyl carbon acids. The alpha-amino carbon at a N-protonated N-terminus of a peptide or protein is estimated to undergo deprotonation about 130-fold faster than the alpha-amino carbon at the corresponding internal amino acid residue. The value of k(HO) for deprotonation of the N-terminal alpha-amino carbon of the glycylglycylglycine zwitterion (pK(a) = 25.1) is similar to that for deprotonation of the more acidic ketone acetone (pK(a) = 19.3), as a result of a lower Marcus intrinsic barrier to deprotonation of cationic alpha-carbonyl carbon acids. The cationic NH(3)(+) group is generally more strongly electron-withdrawing than the neutral NHAc group, but the alpha-NH(3)(+) and the alpha-NHAc substituents result in very similar decreases in the pK(a) of several alpha-carbonyl carbon acids.     

Surface-induced aggregation of beta amyloid peptide by co-substituted alkanethiol monolayers supported on gold

The primary pathological characteristic of Alzheimer's disease is the presence in the brain of self-assembled beta amyloid (Abeta) protein fibrils, consisting of 35-43 amino acid residues. The toxicity of the aggregated protein structures has previously been proposed to be related to the interaction of Abeta fibrils with neuronal membranes (phospholipid bilayers). Here, surfaces consisting of self-assembled alkanethiol monolayers with different end groups--supported on Au--are used to test the effect of surface chemistry on the structure and morphology of aggregates formed from an active fragment (Abeta10-35) of the Abeta peptide. The influence of monolayer nature (end group) on the aggregation of Abeta10-35 was examined using reflection-absorption infrared spectroscopy (RAIRS) and scanning force microscopy (SFM). Evaluation of the SFM and RAIRS data reveals the presence of Abeta10-35 protein on the various monolayer surfaces, with the surface protein possessing predominantly beta-sheet and random-coil conformations. Time-dependent studies of the extent of Abeta10-35 aggregation and deposition on the various surfaces and the effect of the monolayers on seeding of Abeta10-35 aggregates in solution are also discussed.     

Effect of imidazolium-based ionic liquids on the aggregation behavior of twin-tailed cationic gemini surfactant in aqueous solution

Micellization behavior of the twin-tailed surfactants can be modulated by the addition of various modifiers. Ionic liquids (ILs) are one of them and are documented here. The beauty of these environmentally benign neoteric molecules lies in their structural versatility. Here, we have investigated the effect of three ILs: 1-butyl-3-methylimidazolium bromide ([C₄mim][Br]), 1-hexyl-3-methylimidazolium bromide ([C₆mim][Br]), and 1-octyl-3-methylimidazolium bromide ([C₈mim][Br]) on the aggregation and surface adsorption behavior of cationic gemini surfactant, bis(hexadecyldimethyl ammonium)propane dibromide (16-3-16) through experimentally measured electrical conductivities, surface tensions, and by spectral methods (UV-vis absorbance and fluorescence measurements). The main focus of the study is to observe the effect of added ILs on the critical micelle concentration (cmc), various surface parameters, aggregation number, and size of the aggregates of gemini surfactant. The results show that the more hydrophobic ILs, that is, [C₆mim][Br] and [C₈mim][Br] behave as electrolyte at lower concentration and cosurfactant at higher concentration, whereas moderately hydrophobic IL [C₄mim][Br] acts as an electrolyte at all concentration ranges studied. The modulating effects of ILs were also compared with conventional electrolyte (NaBr) at similar conditions.     

Study on the aggregation and electrochemical properties of Rose Bengal in aqueous solution of cyclodextrins

The interactions of Rose Bengal (RB) with alpha-cyclodextrin (alpha-CD), hydroxypropyl-beta-cyclodextrin (HP-beta-CD), hydroxypropyl-gamma-cyclodextrin (HP-gamma-CD), heptakis(2,3,6-tri-O-methyll)-beta-cyclodextrin (TM-beta-CD) were studied in aqueous solutions of 0.1 M KClO(4) and 0.1 M LiClO(4) by vis absorption, fluorescence spectroscopy as well as electrochemical measurements at 298 K. The spectrophometric results indicate that RB is included in all beta- and gamma-CDs forming complexes with a stoichiometry 1:1 whose stability is slightly higher in KClO(4) than in LiClO(4) solutions. The complex stability constants determined for salt-containing CD solutions are lower than those for water solutions. The complexation of RB with beta- and gamma-CD and the differences between the complexes obtained in the presence of the two salts were confirmed by an electrochemical study.