PepMat 2016: The second conference on peptide-based materials for biomedicine and nanotechnology

Postprint (published version

Analog Modeling of Worm-Like Chain Molecules Using Macroscopic Beads-on-a-String

This paper describes an empirical model of polymer dynamics, based on the agitation of millimeter-sized polymeric beads. Although the interactions between the particles in the macroscopic model, and those between the monomers of molecular-scale polymers, are fundamentally different, both systems follow the Worm-Like Chain theory.Chemistry and Chemical BiologyPhysic

Coassembly of Aromatic Dipeptides into Biomolecular Necklaces

This paper describes the formation of complex peptide-based structures by the coassembly of two simple peptides, the diphenylalanine peptide and its tert-butyl dicarbonate (Boc) protected analogue. Each of these peptides can self-assemble into a distinct architecture: the diphenylalanine peptide into tubular structures and its analogue into spheres. Integrated together, these peptides coassemble into a construction of beaded strings, where spherical assemblies are connected by elongated elements. Electron and scanning force microscopy demonstrated the morphology of these structures, which we termed “biomolecular necklaces”. Additional experiments indicated the reversibility of the coassembly process and the stability of the structures. Furthermore, we suggest a possible mechanism of formation for the biomolecular necklaces. Our suggestion is based on the necklace model for polyelectrolyte chains, which proposes that a necklace structure appears as a result of counterion condensation on the backbone of a polyelectrolyte. Overall, the approach of coassembly, demonstrated using aromatic peptides, can be adapted to any peptides and may lead to the development and discovery of new self-assembled architectures formed by peptides and other biomolecules

Probing the Interaction of Individual Amino Acids with Inorganic Surfaces Using Atomic Force Spectroscopy

This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force–distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic–inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices

Structural preferences of an anti-fouling peptide: From single chain to small molecular assemblies

The structural features of a tripeptide constituted by two different non-coded amino acids, 3,4-dihydroxy-L-phenylalanine (L-DOPA) and 4-fluoro-Phenylalanine, (Phe(4F)), have been investigated by means of classical mechanics simulations. This tripeptide had been characterised as an antifouling agent with great adhesion capabilities. In this work, its conformational preferences have been described in two different environments (gas phase and water solution), at three different pHs and with different degrees of terminal capping. At the same time, the structural dynamics of small aggregates of the tripeptide have been investigated and their ability to stabilise ß-sheet based assemblies has been studied. The reported results describe the complexity of the tripeptide conformational preferences due to both the amphiphilic nature of its side chains, and the effect of the ionisation state resulting from the solution conditions. The investigations performed with small tripeptide assemblies in water solution reproduced the previously reported structural features, such as the polymorphism of its aggregates as a function of the pH. At edge pH values, the electrostatic screening imposed by the ions present in the solution facilitates the aggregation of the tripeptide chains, while at neutral pH and low concentrations of ionised species, the polar groups and the hydrogen bond capable groups impose their strength and lead to the disaggregation of the peptide clusters by favouring the solvation of individual chains rather than stabilising the aggregated states.Peer ReviewedPostprint (author's final draft