Kinetic pathways to peptide aggregation on surfaces: the effects of β-sheet propensity and surface attraction

Mechanisms of peptide aggregation on hydrophobic surfaces are explored using molecular dynamics simulations with a coarse-grained peptide representation. Systems of peptides are studied with varying degrees of backbone rigidity (a measure of β-sheet propensity) and degrees of attraction between their hydrophobic residues and the surface. Multiple pathways for aggregation are observed, depending on the surface attraction and peptide β-sheet propensity. For the case of a single-layered β-sheet fibril forming on the surface (a dominant structure seen in all simulations), three mechanisms are observed: (a) a condensation-ordering transition where a bulk-formed amorphous aggregate binds to the surface and subsequently rearranges to form a fibril; (b) the initial formation of a single-layered fibril in the bulk depositing flat on the surface; and (c) peptides binding individually to the surface and nucleating fibril formation by individual peptide deposition. Peptides with a stiffer chiral backbone prefer mechanism (b) over (a), and stronger surface attractions prefer mechanism (c) over (a) and (b). Our model is compared to various similar experimental systems, and an agreement was found in terms of the surface increasing the degree of fibrillar aggregation, with the directions of fibrillar growth matching the crystallographic symmetry of the surface. Our simulations provide details of aggregate growth mechanisms on scales inaccessible to either experiment or atomistic simulations.     

Stabilization of peptide fibrils by hydrophobic interaction

Hydrophobic interactions play an important role in assembly processes in aqueous environments. In case of peptide amphiphiles, hydrophobicity is combined with hydrogen bonding to yield well-defined peptide-based aggregates. Here, we report a systematic study after the role of hydrophobic interactions on both stabilization and morphology of a peptide fibrillar assembly. For this purpose, alkyl tails were connected to a known beta-sheet forming peptide with the sequence KTVIIE. The introduction of n-alkyl groups induced thermal stability to the assemblies without affecting the morphology of the peptide aggregates.     

Cooperative and reciprocal chiral structure formation of an alanine-based peptide confined at the surface of cationic surfactant membranes

The confinement of anionic oligoalanine peptides at the surface of cationic membranes can cooperatively reinforce peptide/peptide interactions and induce secondary-structure formation, and, reciprocally, induce chirality expression of the membrane at the mesoscopic level, thus leading to the formation of three-dimensional chiral fibrillar networks. Such a strong binding effect of peptides with cationic membranes and the resulting cooperative assembly behaviors are observed with two different types of cationic surfactant, namely, two-head two-tail gemini and one-head two-tail surfactants. The ensemble of assembly properties, such as critical micellar concentration (cmc), Krafft temperature (T(k) ), molecular area at the air/water interface, molecular organization (as studied by FTIR attenuated total reflectance (ATR) measurements and small-angle X-ray scattering), and morphology of the aggregates (as observed by optical and electron microscopy studies), are reported. The results clearly demonstrate that the molecular organization and mesoscopic supramolecular structures are controlled by a subtle balance between the peptide/peptide interactions, ionic interactions between the membranes and peptides, and the interactions the between surfactant molecules, which are governed by hydrophobicity and steric interactions. Investigation into such cooperative organization can shed light on the mechanism of supramolecular chirality expression in membrane systems and allow understanding of the structure of peptides in interactions with lipid bilayers.     

DNA melting in aggregates: impeded or facilitated?

How does DNA melt in columnar aggregate relative to its melting in diluted solution? Is the melting temperature increased or decreased with the aggregate density? Have DNA-DNA interactions, predominantly of electrostatic nature, an effect on the character of the melting transition? In attempt to answer these questions, we have incorporated the theory of electrostatic interactions between DNA duplexes into the simplest model of DNA melting. The analysis shows that the effect of aggregate density is very different for aggregates built of homologous (or identical) DNA fragments relative to the case of DNA with random base pair sequences. The putative attraction between homologous DNA helices hampers their melting and increases the melting temperature and can even dramatically change the character of the transition. In the aggregate of nonhomologous DNAs, the pattern of electrostatic interactions is more complicated, and their effect could be opposite; in some cases we may even expect electrostatically induced melting. These findings define new directions for melting experiments in dense DNA assemblies.     

The controlled flocculation of submicron emulsion particles. I. A three-step synthetic route to supermicron polymer particles

The basic features of a three-step experimental process to produce supermicron polymer particles are described. First, a submicron emulsifier-free latex is prepared by a well-known technique. Second, the latex is aggregated by destabilizing with cetyl pyridinium chloride under constant stirring conditions, to yield roughly spherical clusters of 6-12 μ diameter. Third, the aggregates are stabilized with poly(vinyl alcohol) and internally coalesced by heating at or above the glass transition temperature. The final product particles have relatively smooth surfaces. Results are qualitatively interpreted in terms of a dynamic equilibrium where the aggregate size is determined by a balance between attractive interparticle potentials and stirring shear forces. Bimodal aggregate size distributions suggest the aggregate break-up mechanism may involve the erosion of individual latex particles and small fragments from the surface of aggregates. © 1996 John Wiley & Sons, Inc.     

Morphological studies of blends of conjugated polymers and acceptor molecules using langevin dynamics simulations

We use coarse‐grained Langevin dynamics simulations of blends of generic conjugated polymers and acceptor molecules to show how architecture (e.g., side chains, backbone flexibility of oligomers) and the pair‐wise interactions between the constituents of the blend affect morphology and phase transition. Alkyl side chains on the conjugated oligomer backbones shift the liquid crystal (LC) transition temperature from that of bare conjugated backbones and the direction of the shift depends on backbone–backbone interactions. Rigid backbones and constrained side chains cause a layer‐by‐layer morphology of conjugated polymers and amorphous acceptors, whereas flexible backbones and unconstrained side chains facilitate highly ordered acceptor arrangement. Strong backbone–backbone attraction shifts LC transition to higher temperatures than weak backbone–backbone attraction, and strong acceptor–acceptor attraction increases acceptor aggregation. Pure macro‐phase separated domains form when all pair‐wise interactions in the blend are strongly attractive, whereas interconnected domains form at intermediate acceptor–acceptor attraction and strong polymer–polymer attractions. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Aggregation Pathways of the Amyloid β(1-42) Peptide Depend on Its Colloidal Stability and Ordered β-Sheet Stacking

Amyloid β (Aβ) fibrils are present as a major component in senile plaques, the hallmark of Alzheimer's disease (AD). Diffuse plaques (nonfibrous, loosely packed Aβ aggregates) containing amorphous Aβ aggregates are also formed in brain. This work examines the influence of Cu(2+) complexation by Aβ on the aggregation process in the context of charge and structural variations. Changes in the surface charges of Aβ molecules due to Cu(2+) binding, measured with a ζ-potential measurement device, were correlated with the aggregate morphologies examined by atomic force microscopy. As a result of the charge variation, the "colloid-like" stability of the aggregation intermediates, which is essential to the fibrillation process, is affected. Consequently, Cu(2+) enhances the amorphous aggregate formation. By monitoring variations in the secondary structures with circular dichroism spectroscopy, a direct transformation from the unstructured conformation to the β-sheet structure was observed for all types of aggregates observed (oligomers, fibrils, and/or amorphous aggregates). Compared to the Aβ aggregation pathway in the absence of Cu(2+) and taking other factors affecting Aβ aggregation (i.e., pH and temperature) into account, our investigation indicates that formations of amorphous and fibrous aggregates diverge from the same β-sheet-containing partially folded intermediate. This study suggests that the hydrophilic domain of Aβ also plays a role in the Aβ aggregation process. A kinetic model was proposed to account for the effects of the Cu(2+) binding on these two aggregation pathways in terms of charge and structural variations.     

The dynamic nature of incubation solution after cooling to room temperature in amyloid formation of hen egg white lysozyme: An FTIR assessment

Amyloid formation of hen egg white lysozyme (HEWL) usually requires elevated temperature, while biophysical characterizations on the incubation solution are often performed at room temperature. Whether maintaining the incubation solution at room temperature results in further structural changes is a significantly important issue that has never been explored. Herein, we use FTIR spectroscopy to assess this issue and reveal that the hot incubation solution of HEWL after cooling to room temperature is in a dynamically evolving state and forms β-sheet aggregates continuously over time. Combined with AFM, we show that these aggregates are non-fibrillar β-sheet aggregates and have vibrational signature distinct from that of fibrillar aggregates. Using FTIR difference spectroscopy, we demonstrate that these non-fibrillar aggregates are in an anti-parallel β-sheet configuration. We also provide a detailed discussion on the spectral assignments for protein aggregates in anti-parallel and parallel β-sheet configurations. With FTIR second derivative technique, we show that these non-fibrillar aggregates are in fact present along with fibrillar aggregates during incubation under elevated temperature but are less stable compared with that at room temperature. Implications from the current work are discussed.     

First crystallographic signature of amyloid-like fibril forming beta-sheet assemblage from a tripeptide with non-coded amino acids

The model tripeptide Boc-beta-Ala(1)-Aib(2)-beta-Ala(3)-OMe 1 [beta-Ala: beta-alanine, Aib: alpha-aminoisobutyric acid] forms an infinite parallel beta-sheet structure through intermolecular interactions in single crystals and from the SEM diagram of this peptide, it is evident that the compound has fibrillar morphology, a characteristic of neurodegenerative disease causing amyloid aggregate.     

Aggregation between xanthan and nonyphenyloxypropyl beta-hydroxyltrimethylammonium bromide in aqueous solution: MesoDyn simulation and binding isotherm measurement

The aggregation behavior of nonyphenyloxypropyl beta-hydroxyltrimethylammonium bromide (C9phNBr) and xanthan (XC) in aqueous solution was investigated by MesoDyn density functional simulation and binding isotherm measurement. The process of aggregate formation and the aggregate morphology are reported. The formation of aggregates includes three stages and the morphology of XC-C9phNBr aggregates is rodlike or ellipsoidal. The effects of temperature and XC concentration on the aggregation are analyzed. Results indicate that the formation of aggregates is an exothermic process, and their formation becomes more difficult and the formation rate decreases with increasing temperature. The formation of aggregates is also related to XC concentration, and it becomes much more difficult when the concentration of XC is higher than 20 vol %. The simulation results agree with binding isotherms of C9phNBr to XC obtained via the potentiometric titration method, which shows a typical cooperative binding between C9phNBr and XC.     

Influence of surface interactions on folding and forced unbinding of semiflexible chains

We have investigated the folding and forced unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe, at an elementary level, a number of biologically relevant phenomena that include adhesive interactions between proteins and tethering of receptors to cell walls. The binding interface is modeled as a solid surface, and the wormlike chain (WLC) is used for the semiflexible chain (SC). Using Langevin simulations, in the overdamped limit we examine the ordering kinetics of racquet-like and toroidal structures in the presence of an attractive interaction between the surface and the polymer chain. For a range of interactions, temperature, and the persistence length, l(p), we obtained the monomer density distribution, n(x), (x is the perpendicular distance of a tagged chain end from the surface) for all of the relevant morphologies. There is a single peak in n(x) inside the range of attractive forces, b, for chains in the extended conformations, whereas in racquet and toroidal structures there is an additional peak at x approximately b. The simulated results for n(x) are in good agreement with theory. The formation of toroids on the surface appears to be a first-order transition as evidenced by the bimodal distribution in n(x). The theoretical result underestimates the simulated n(x) for x < b and follows n(x) closely for x >/= b; the calculated density agrees exactly with n(x) in the range x < b. The chain-surface interaction is probed by subjecting the surface structures to a pulling force, f. The average extension, x( f), as a function of f exhibits a sigmoidal profile with sharp all-or-none transition at the unfolding force threshold f = f(c) which increases for more structured states. Simulated x(f) compare well with the theoretical predictions. The critical force, f(c), is a function of l(s)/l(c) for a fixed temperature, where l(c) and l(s) are the length scales that express the strength of the intramolecular and SC-surface attraction, respectively. For a fixed l(s), f(c) increases as l(p) decreases.     

Unusual vesicle-micelle transitions in a salt-free catanionic surfactant: temperature and concentration effects

The spontaneous formation of vesicles by the salt-free surfactant hexadecyltrimethylammonium octylsulfonate (TASo) and the features of an unusual vesicle-micelle transition are investigated in this work. In a previous work, we have shown that this highly asymmetric catanionic surfactant displays a rare lamellar miscibility gap in the concentrated regime. Here, we analyze in detail the aggregation behavior in the dilute regime (less than 3 wt % surfactant) as a function of both concentration and temperature. The phase diagram is dominated by a two-phase region consisting of a dispersion of a swollen lamellar phase (Lalpha') in the excess solvent phase (L1). Stable vesicles form in this two-phase region, and upon temperature increase, a transition to a single solution phase containing only elongated micelles occurs. The structural characterization of the aggregates and the investigation of their equilibrium properties have been carried out by light microscopy, cryo-TEM, water self-diffusion NMR, and SANS. Similarly to the lamellar-lamellar coexistence, the changes in microstructure at high dilution and high temperature can be understood from solubility differences, electrostatic interactions, and preferred aggregate curvature. Surface charge in the aggregates stems from the higher solubility of the octylsulfonate (So-) ion as compared to that of the hexadecyltrimethylammonium ion (TA+). Upon temperature increase, the ratio of free So(-) relative to the neutral TASo increases. Consequently, the surface charge density of the aggregates increases, and this ultimately induces a transition to a higher-curvature morphology (elongated micelles). Vesicles can also be spontaneously formed by cooling solutions from the micellar region, and the mean size obtained is practically independent of cooling rate, suggesting that dissociation/charge effects also control this process.     

Molecular dynamics simulations of polyelectrolyte-polyampholyte complexes. Effect of solvent quality and salt concentration

Complexation between polyelectrolyte and polyampholyte chains in poor solvent conditions for the polyelectrolyte backbone has been studied by molecular dynamics simulations. In a poor solvent a polyelectrolyte forms a necklace-like structure consisting of polymeric globules (beads) connected by strings of monomers. The simulation results can be explained by assuming the existence of two different mechanisms leading to the necklace formation. In the case of weak electrostatic interactions, the necklace formation is driven by optimization of short-range monomer-monomer attraction and electrostatic repulsion between charged monomers on the polymer backbone. In the case of strong electrostatic interactions, the necklace structure appears as a result of counterion condensation. While the short-range attractions between monomers are still important, the correlation-induced attraction between condensed counterions and charged monomers and electrostatic repulsion between uncompensated charges provide significant contribution to optimization of the necklace structure. Upon forming a complex with both random and diblock polyampholytes, a polyelectrolyte chain changes its necklace conformation by forming one huge bead. The collapse of the polyelectrolyte chain occurs due to the neutralization of the polyelectrolyte charge by polyampholytes. In the case of the random polyampholyte, the more positively charged sections of the chain mix with negatively charged polyelectrolyte forming the globular bead while more negatively charged chain sections form loops surrounding the collapsed core of the aggregate. In the case of diblock polyampholyte, the positively charged block, a part of the negatively charged block, and a polyelectrolyte chain form a core of the aggregate with a substantial section of the negatively charged block sticking out from the collapsed core of the aggregate. In both cases the core of the aggregate has a layered structure that is characterized by the variations in the excess of concentration of monomers belonging to polyampholyte and polyelectrolyte chains throughout the core radius. These structures appear as a result of optimization of the net electrostatic energy of the complex and short-range attractive interactions between monomers of the polyelectrolyte chain.     

Amyloid-like fibril-forming supramolecular β-sheets from a β-turn forming tripeptide containing non-coded amino acids: the crystallographic signature

The crystal structure of a terminally protected tripeptide Boc-Leu-Aib-β-Ala-OMe 1 containing non-coded amino acids reveals that it adopts a β-turn structure, which self-assembles to form a supramolecular β-sheet via non-covalent interactions. The SEM image of peptide 1 exhibits amyloid-like fibrillar morphology in the solid state.     

The interaction between charged aggregates in electrolyte solution. A Monte Carlo simulation study

The Monte Carlo simulation technique has been used to calculate the electrostatic force acting upon a charged aggregate outside a similarly charged wall. Contrary to intuition and existing electrostatic theories, the force is found to be attractive for some realistic values of the parameters determining the system. High surface charge density, low temperature, low relative permitivity and polyvalent neutralizing counterions are all factors that favour a net attraction between the wall and the aggregate. In some cases the resulting electrostatic attractive force is found to be an order of magnitude larger than the ordinary van der Waals attraction applied in the DLVO theory of colloidal stability. The attractive interaction is interpreted as being due to currelations between the counterions in the electric double layers.     

Selective adsorption of block copolymers on patterned surfaces

Adsorption of copolymers on patterned surfaces is studied using lattice modeling and multiple Markov chain Monte Carlo methods. The copolymer is composed of alternating blocks of A and B monomers, and the adsorbing surface is composed of alternating square blocks containing C and D sites. Effects of interaction specificity on the adsorbed pattern of the copolymer and the sharpness of the adsorption transition are investigated by comparing three different models of copolymer-surface interactions. Analyses of the underlying energy distribution indicate that adsorption transitions in our models are not two-state-like. We show how the corresponding experimental question may be addressed by calorimetric measurements as have been applied to protein folding. Although the adsorption transitions are not "first order" or two-state-like, the sharpness of the transition increases when interaction specificity is enhanced by either including more attractive interaction types or by introducing repulsive interactions. Uniformity of the pattern of the adsorbed copolymer is also sensitive to the interaction scheme. Ramifications of the results from the present minimalist models of pattern recognition on the energetic and statistical mechanical origins of undesirable nonspecific adsorption of synthetic biopolymers in cellular environments are discussed.     

Stoichiometric inhibition of amyloid beta-protein aggregation with peptides containing alternating alpha,alpha-disubstituted amino acids

We have prepared two peptides based on the hydrophobic core (Lys-Leu-Val-Phe-Phe) of amyloid beta-protein (Abeta) that contain alpha,alpha-disubstituted amino acids at alternating positions, but differ in the positioning of the oligolysine chain (AMY-1, C-terminus; AMY-2, N-terminus). We have studied the effects of AMY-1 and AMY-2 on the aggregation of Abeta and find that, at stoichiometric concentrations, both peptides completely stop Abeta fibril growth. Equimolar mixtures of AMY-1 and Abeta form only globular aggregates as imaged by scanning force microscopy and transmission electron microscopy. These samples show no signs of protofibrillar or fibrillar material even after prolonged periods of time (4.5 months). Also, 10 mol % of AMY-1 prevents Abeta self-assembly for long periods of time; aged samples (4.5 months) show only a few protofibrillar or fibrillar aggregates. Circular dichroism spectroscopy of equimolar mixtures of AMY-1 and Abeta show that the secondary structure of the mixture changes over time and progresses to a predominantly beta-sheet structure, which is consistent with the design of these inhibitors preferring a sheet-like conformation. Changing the position of the charged tail on the peptide, AMY-2 interacts with Abeta differently in that equimolar mixtures form large ( approximately 1 mum) globular aggregates which do not progress to fibrils, but precipitate out of solution. The differences in the aggregation mediated by the two peptides is discussed in terms of a model where the inhibitors act as cosurfactants that interfere with the native ability of Abeta to self-assemble by disrupting hydrophobic interactions either at the C-terminus or N-terminus of Abeta.     

Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials

We present a simple and highly adaptable method for simulating coarse-grained lipid membranes without explicit solvent. Lipids are represented by one head bead and two tail beads, with the interaction between tails being of key importance in stabilizing the fluid phase. Two such tail-tail potentials were tested, with the important feature in both cases being a variable range of attraction. We examined phase diagrams of this range versus temperature for both functional forms of the tail-tail attraction and found that a certain threshold attractive width was required to stabilize the fluid phase. Within the fluid-phase region we find that material properties such as area per lipid, orientational order, diffusion constant, interleaflet flip-flop rate, and bilayer stiffness all depend strongly and monotonically on the attractive width. For three particular values of the potential width we investigate the transition between gel and fluid phases via heating or cooling and find that this transition is discontinuous with considerable hysteresis. We also investigated the stretching of a bilayer to eventually form a pore and found excellent agreement with recent analytic theory.     

Transition from thermodynamically stable solution to colloid dispersion state

In this work, we investigated the transition between solution and dispersion state of the poly-N-isopropylacrylamide microgel latex. The aggregation state of the colloid system was described by applying the multiple chemical equilibrium model. The model predicts that in the case of ordinary colloid dispersions, formation of small equilibrium aggregates cannot be expected in the practically accessible concentration range. However, when the particle–particle attraction is small enough, then formation of finite size aggregates in equilibrium with the monomers may take place. To test the model, the aggregation behavior of a temperature-sensitive soft colloid dispersion (poly-N-isopropylacrylamide microgels) was investigated for which the attractive interactions could be precisely controlled by the temperature of the system. The experimental results provide a support for the theoretical predictions.     

Dependence of Self-Assembled Peptide Hydrogel Network Structure on Local Fibril Nanostructure

Physically cross-linked, fibrillar hydrogel networks are formed by the self-assembly of β-hairpin peptide molecules with varying degrees of strand asymmetry. The peptide registry in the self-assembled state can be used as a design element to generate fibrils with twisting, nontwisting, or laminated morphology. The mass density of the networks varies significantly, and can be directly related to the local fibrillar morphology as evidenced by small angle neutron scattering (SANS) and in situ substantiation using cryogenic transmission electron microscopy (cryo-TEM) under identical concentrations and conditions. Similarly, the density of the network is dependent on changes in the peptide concentration. Bulk rheological properties of the hydrogels can be correlated to the fibrillar nanostructure, with the stiffer, laminated fibrils forming networks with a higher G' as compared to the flexible, singular fibrillar networks.