Irina A. Nyrkova

Engineering of peptide β-sheet nanotapes

A set of principles are outlined for the design of short oligopeptides which will self-assemble in appropriate solvents into long, semi-flexible, polymericβ-sheet nanotapes. Their validity is demonstrated by experimental studies of an 11-residue peptide (DN1) which forms nanotapes in water, and a 24-residue peptide (K24) which forms nanotapes in non-aqueous solvents such as methanol. Circular dichroism (CD) spectroscopy studies of the self-assembly behaviour in very dilute solutions (µm) reveal a simple transition from a random coil-to-β-sheet conformation in the case of DN1, but a more complex situation for K24. Association of DN1 is very weak up to a concentration of 40 µm at which there is a sudden increase in the fraction of peptide in the β-sheet structure, indicative of an apparent ‘critical tape concentration’. This is shown to arise from a two-step self-assembly process: the first step being a transition from a random coil to an extended β-strand conformation, and the second the addition of this β-strand to a growing β-sheet. Both peptides are shown to gel their solvents at concentrations above 2×10 -3 volume fraction: these gels are stable up to the boiling point of the solvents. Rheology measurements on gels of the 24-residue peptide in 2-chloroethanol reveal that the tapes form an entangled network with a mesh size of 10–100 nm for peptide volume fractions 0.03–0.003; the persistence length of the tape is 13 nm or greater, indicative of a moderately rigid polymer; the tapes are about a single molecule in thickness. The mechanical properties of the gels in many respects are comparable to those of natural biopolymers such as gelatin, actin, amylose and agarose.

Anisotropic Self-Assembly of Supramolecular Polymers and Plasmonic Nanoparticles at the Liquid–Liquid Interface

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.

Simple one‐particle diffusional model to mimic some properties of the glass transition

A new simplified model is proposed to mimic some properties of the glass transition. The physical system undergoing glass transition is modeled as Brownian particle diffusing in one‐ or two‐dimensional space with obstacles. In one dimension obstacles are points which cannot be crossed by Brownian particles, in two dimensions obstacles are randomly distributed sections of straight lines which are impenetrable for the diffusing particle. The obstacles have a finite lifetime τ. After time τ the obstacle disappears and reappears in some new random position. In another modification of the model the obstacle barrier can be opened for short time and then closed again. Both cases are studied for one‐dimensional diffusion, while in two dimensions only the first modification of the model is considered. The main feature of the model is that the mean lifetime of obstacles τ is connected with the diffusion coefficient of the Brownian particle through the coupling equation Dτ=K, with K being the coupling constant. This...

Statistics of an ideal polymer chain near the bifurcation region of a narrow tube

Conformational statistics of an ideal polymer chain in the vicinity of the bifurcation region of a narrow pore system is considered. It is shown that the bifurcation region plays the role of an effective entropic trap. Due to this fact the chain adopts globular conformation with the average dimensions of the order of the dimensions of the bifurcation region. It is concluded that the statistical properties of an ideal polymer chain and of random walks near the bifurcation point are essentially different.

Peptide strand length controls the energetics of self-assembly and morphology of β-sheet fibrils

Self‐assembling peptides can be used as versatile, natural, and multifunctional building blocks to produce a variety of well‐defined nanostructures, materials and devices for applications in medicine and nanotechnology. Here, we concentrate on the 1D self‐assembly of de novo designed Px‐2 peptide β‐strands into anti‐parallel β‐sheet tapes and higher order aggregates. We study six members of the Px‐2 family, ranging from 3 amino acids (aa) to 13 aa in length, using a range of complementary experimental techniques, computer simulation and theoretical statistical mechanics. The critical concentration for self‐assembly (c*) is found to increase systematically with decreasing peptide length. The shortest peptide found to self‐assemble into soluble β‐tapes in water is a 5 amino acid residue peptide. These investigations help decipher the role of the peptide length in controlling self‐assembly, aggregate morphology, and material properties. By extracting free energies from these data using a statistical mechanical analysis and combining the results with computer simulations at the atomistic level, we can extract the entropy of association for individual β‐strands.