Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics.
ABSTRACT: Self-assembly at a liquid-liquid interface is a powerful experimental route to novel nanomaterials. We report herein a computational study of peptide nanotube formation at an oil-water interface. We probe interfacial self-assembly and nanotube formation of the cyclic octapeptide, cyclo [(-L-Trp-D-Leu-)4] as an illustrative example. Individual peptide rings are rapidly adsorbed at the liquid-liquid interface where they self-assemble. Monomeric and dimeric peptide rings lie with their molecular planes mostly parallel to the interface. Longer oligomeric nanotubes are increasingly tilted at the interface and grow by an Oswald ripening mechanism to eventually align their tube axis parallel to the interface. The present results on nanotube assembly suggest that computation will be a useful complement to experiment in understanding the nature of self-assembly of nanomaterials at liquid-liquid interfaces.
Project description:Hybridizing carbon nanomaterials (CNMs) with amyloid fibrils-the ordered nanostructures self-assembled by amyloidogenic peptides-has found promising applications in bionanotechology. Understanding fundamental interactions of CNMs with amyloid peptides and uncovering the determinants of their self-assembly structures and dynamics are, therefore, pivotal for enriching and enabling this novel class of hybrid nanomaterials. Here, we applied atomistic molecular dynamics simulations to investigate the self-assembly of two amyloid peptides-the amyloidogenic core residues 16-22 of amyloid-? (A?16-22) and the non-amyloid-? core of ?-synuclein (NACore68-78)-on the surface of carbon nanotubes (CNT) with different sizes and chirality. Our computational results showed that with small radial CNTs, both types of peptides could form ?-sheets wrapping around the nanotube surface into a supercoiled morphology. The angle between ?-strands and nanotube axes in the supercoil structure depended mainly on the peptide sequence and CNT radius, but also weakly on the CNT chirality. Large radial CNTs and the extreme case of the flat graphene nanosheet, on the other hand, could nucleate amyloid fibrils perpendicular to the surface. Our results provided new insights of hybridizing CNMs with amyloid peptides and also offered a novel approach to manipulate the morphology of CNM-induced amyloid assembly by tuning the surface curvature, peptide sequence, and molecular ratio between peptides and available CNM surface area, which may be useful in engineering nanocomposites with high-order structures.
Project description:Though nanomaterials such as carbon nanotubes have gained recent attention in biology and medicine, there are few studies at the single-molecule level that explore their interactions with disease-causing proteins. Using atomistic molecular-dynamics simulations, we have investigated the interactions of the monomeric A?(1-42) peptide with a single-walled carbon nanotube of small diameter. Starting with peptide-nanotube complexes that delineate the interactions of different segments of the peptide, we find rapid convergence in the peptide's adsorption behavior on the nanotube surface, manifested in its arrested movement, the convergence of peptide-nanotube contact areas and approach distances, and in increased peptide wrapping around the nanotube. In systems where the N-terminal domain is initially distal from nanotube, the adsorption phenomena are initiated by interactions arising from the central hydrophobic core, and precipitated by those arising from the N-terminal residues. Our simulations and free energy calculations together demonstrate that the presence of the nanotube increases the energetic favorability of the open state. We note that the observation of peptide localization could be leveraged for site-specific drug delivery, while the decreased propensity of collapse appears promising for altering kinetics of the peptide's self-assembly.
Project description:Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for ?-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for ?-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.
Project description:There is overwhelming evidence that ions are present near the vapor-liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion-ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor-liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. "Sticky" electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from ?-helical to a hairpin-turn-like one in response to charging of its ends.
Project description:Quantitatively understanding the self-assembly of amphiphilic macromolecules at liquid-liquid interfaces is a fundamental scientific concern due to its relevance to a broad range of applications including bottom-up nanopatterning, protein encapsulation, oil recovery, drug delivery, and other technologies. Elucidating the mechanisms that drive assembly of amphiphilic macromolecules at liquid-liquid interfaces is challenging due to the combination of hydrophobic, hydrophilic, and Coulomb interactions, which require consideration of the dielectric mismatch, solvation effects, ionic correlations, and entropic factors. Here we investigate the self-assembly of a model block copolymer with various charge fractions at the chloroform-water interface. We analyze the adsorption and conformation of poly(styrene)-block-poly(2-vinylpyridine) (PS-b-P2VP) and of the homopolymer poly(2-vinylpyridine) (P2VP) with varying charge fraction, which is controlled via a quaternization reaction and distributed randomly along the backbone. Interfacial tension measurements show that the polymer adsorption increases only marginally at low charge fractions (<5%) but increases more significantly at higher charge fractions for the copolymer, while the corresponding randomly charged P2VP homopolymer analogues display much more sensitivity to the presence of charged groups. Molecular dynamics (MD) simulations of the experimental systems reveal that the diblock copolymer (PS-b-P2VP) interfacial activity could be mediated by the formation of a rich set of complex interfacial copolymer aggregates. Circular domains to elongated stripes are observed in the simulations at the water-chloroform interface as the charge fraction increases. These structures are shown to resemble the spherical and cylindrical helicoid structures observed in bulk chloroform as the charge fraction increases. The self-assembly of charge-containing copolymers is found to be driven by the association of the charged component in the hydrophilic block, with the hydrophobic segments extending away from the hydrophilic cores into the chloroform phase.
Project description:Achieving the co-assembly of more than one component represents an important challenge in the drive to create functional self-assembled nanomaterials. Multicomponent nanomaterials comprised of several discrete, spatially sorted domains of components with high degrees of internal order are particularly important for applications such as optoelectronics. In this work, single-walled carbon nanotubes (SWNTs) were threaded through the inner channel of nanotubes formed by the bolaamphiphilic self-assembly of a naphthalenediimide-lysine (NDI-Bola) monomer. The self-assembly process was driven by electrostatic interactions, as indicated by ?-potential measurements, and cation-? interactions between the surface of the SWNT and the positively charged, NDI-Bola nanotube interior. To increase the threading efficiency, the NDI-Bola nanotubes were fragmented into shortened segments with lengths of <100 nm via sonication-induced shear, prior to co-assembly with the SWNTs. The threading process created an initial composite nanostructure in which the SWNTs were threaded by multiple, shortened segments of the NDI-Bola nanotube that progressively re-elongated along the SWNT surface into a continuous radial coating around the SWNT. The resultant composite structure displayed NDI-Bola wall thicknesses twice that of the parent nanotube, reflecting a bilayer wall structure, as compared to the monolayer structure of the parent NDI-Bola nanotube. As a final, co-axial outer layer, poly(p-phenyleneethynylene) (PPE-SO3Na, M W = 5.76 × 104, PDI - 1.11) was wrapped around the SWNT/NDI-Bola composite resulting in a three-component (SWNT/NDI-Bola/PPE-SO3Na) composite nanostructure.
Project description:Thin films of MoS2 bilayer nanoflakes, which are predominantly a single flake thick and with flakes in edge-to-edge contact, have been produced via self-assembled tiling at the planar interface between two immiscible liquids. Films of several square centimeters extent can be produced with a total covered area approaching 90% and over 70% of the film covered by single flakes without overlap. Films produced through liquid/liquid assembly are shown to produce a lower uncovered area fraction and more uniform thickness when compared with films of similar areal coverage produced by the "top-down" techniques of spin coating and spray coating. Statistical analysis of flake coverage data, measured by atomic force microscopy (AFM), shows that liquid/liquid assembly produces a distinctly different variation in film thickness than conventional top-down deposition. This supports the hypothesis that the two-dimensional (2D) confinement of liquid/liquid assembly produces more uniform films. Demonstrator field-effect transistors (FETs) manufactured from the films exhibit mobility and on/off current ratios of 0.73 cm2 V-1 s-1 and 105, respectively, comparable to FETs of similar layout and chemical vapor deposition (CVD)-grown or mechanically cleaved single-crystal MoS2 channel material. This work demonstrates the use of liquid/liquid interfaces as a useful tool for the self-assembly of high-performance thin-film devices made from dispersions of 2D materials.
Project description:An important goal of the modern soft matter science is to discover new self-assembly modalities to precisely control the placement of small particles in space. Spatial inhomogeneity of liquid crystals offers the capability to organize colloids in certain regions such as the cores of the topological defects. Here we report two self-assembly modes of nanoparticles in linear defects-disclinations in a lyotropic colloidal cholesteric liquid crystal: a continuous helicoidal thread and a periodic array of discrete beads. The beads form one-dimensional arrays with a periodicity that matches half a pitch of the cholesteric phase. The periodic assembly is governed by the anisotropic surface tension and elasticity at the interface of beads with the liquid crystal. This mode of self-assembly of nanoparticles in disclinations expands our ability to use topological defects in liquid crystals as templates for the organization of nanocolloids.
Project description:The study of supramolecular polymers in the bulk, in diluted solution, and at the solid-liquid interface has recently become a major topic of interest, going from fundamental aspects to applications in materials science. However, examples of supramolecular polymers at the liquid-liquid interface are mostly unexplored. Here, we describe the supramolecular polymerization of triarylamine molecules and their light-triggered organization at a chloroform-water interface. The resulting interfacial nematic layer of these 1D supramolecular polymers is further used as a template for the precise alignment of spherical gold nanoparticles coming from the water phase. These hybrid thin films are spontaneously formed in a single process, without chemical prefunctionalization of the metallic nanoparticles, and their ordering is improved by centrifugation. The resulting polymer chains and strings of nanoparticles can be co-aligned with high anisotropy over very large distances. By using a combination of experimental and theoretical investigations, we decipher the full sequence of this oriented self-assembly process. In such a highly anisotropic configuration, electron energy loss spectroscopy reveals that the self-assembled nanoparticles behave as plasmonic waveguides.
Project description:Self-assembly of short peptides into nanostructures has become an important strategy for the bottom-up fabrication of nanomaterials. Significant interest to such peptide-based building blocks is due to the opportunity to control the structure and properties of well-structured nanotubes, nanofibrils, and hydrogels. X-ray crystallography and solution NMR, two major tools of structural biology, have significant limitations when applied to peptide nanotubes because of their non-crystalline structure and large weight. Polarized Raman spectroscopy was utilized for structural characterization of well-aligned D-Diphenylalanine nanotubes. The orientation of selected chemical groups relative to the main axis of the nanotube was determined. Specifically, the C-N bond of CNH3+groups is oriented parallel to the nanotube axis, the peptides' carbonyl groups are tilted at approximately 54° from the axis and the COO- groups run perpendicular to the axis. The determined orientation of chemical groups allowed the understanding of the orientation of D-diphenylalanine molecule that is consistent with its equilibrium conformation. The obtained data indicate that there is only one orientation of D-diphenylalanine molecules with respect to the nanotube main axis.