Supramolecular systems chemistry using peptides

Living systems possess overwhelming molecular complexity that largely results from combinations of just twenty amino acids that are found across all life forms (the building blocks of life). Complexity of proteins arises from combinations of hundreds amino acid building blocks, where self-assembly dictates structure and functionality. Apart from their vital role on building living processes, short peptide sequences (minimalistic version of more complex biological machinery, consisted of 2-6 amino acids), appear to be ideal structural candidates for the fabrication of soft nanomaterials, with potential applications in food, cosmetics and nanomedicine. Supramolecular systems can be classified into three distinct types of self-assembly, based on the way that precursors and self-assembling building blocks relate in the free energy diagram. Thermodynamically driven supramolecular systems, resulting in the formation of permanent supramolecular assemblies, where the self-assembly pathway and the final supramolecular state is irrelevant. The self-assembly pathway becomes a crucial factor for kinetically controlled supramolecular systems, with the structures formed, representing local minima in the free energy landscapes. Finally, away-from-equilibrium chemical systems, systems that transiently exist only under the influence of constant chemical energy (fuel) and when the energy runs out, the system relaxes back to the initial unassembled state. In the first part of the thesis, we demonstrate the use of mechanical energy (high oscillating pressure waves-ultrasonic frequencies of 80.000 Hz) to trigger anisotropy and the formation of highly ordered supramolecular architectures. This is achieved by using tripeptide sequences with D-stereoisomer in the N-terminus of the sequence, where the use of ultrasound gives rise to the formation of gels with enhanced supramolecular properties, as evidenced using spectroscopic (FT-IR, CD, LD) and microscopic techniques (TEM, SEM). Subsequently, ultrasound was used to transiently affect supramolecular systems. In this case, the mechanical energy was used to trigger temporary supramolecular reconfiguration of aromatic dipeptide amphiphiles. The supramolecular transitions observed were due to an alter balance of hydrophobic and H-bonding type interactions that drive the assembly of aromatic peptide amphiphiles. Notably, a direct comparison between thermal heating and mechanical energy is also demonstrated, which relates the directional and oscillating characteristics of ultrasound, when it is used to locally deliver heat into a system.;Responsiveness, functionality and adaptability are further demonstrated using different stimuli. Biocatalytic self-assembly has been utilised to direct supramolecular systems. Thermodynamically driven biocatalytic self-assembly is used to achieve morphological control (fibres, sheets and tubes) on aromatic dipeptide amphiphiles, via minimal stereo-electronic substitution on the para position of the phenylalaline amino acid residue. The control of the resultant supramolecular nanostructures and properties arises from the relative importance of stacking interactions among the aromatics and H-bonding between the dipeptide backbones. The concept of thermodynamically driven biocatalytic self-assembly is further utilised to direct the formation of Dynamic Peptide Libraries (DPLs). The amino acids within a dipeptide sequence are exchanged dynamically using in situ catalytic synthesis and hydrolysis of amide bonds, where the free energy involved in selfassembly of the nanostructure provides the driving force for its formation. The use of searchable dynamic peptide libraries gives rise to the ability to explore the structural sequences space of short peptides. Selective catalytic amplification is achieved through an interplay with environmental triggers. Differential formation of peptide subunits (library members), accompanied with structural reconfiguration is favored in the presence of different environment, such as solvents and salts. Additionally, a direct comparison between biocatalytically driven formation of different molecular species and chemically synthesized assemblies is used to show that shape control may be achieved. Biocatalytic self-assembly is also used to trigger the formation of non-equilibrium transient supramolecular systems. In this case, structural adaption is achieved based on biocatalytic formation and hydrolysis of self-assembling tripeptides, which catalyzed by chymotrypsin, starting from a simple dipeptide methyl ester, the wellknown sweetener, aspartame. The chemical design dictates the kinetics and the consequent lifetime of the nanostructures formed, which can be refueled several times by the addition of the fuel (aspartame), where the fibres are continuously forming and shortening, indicating a dynamically unstable system. This thesis ends with a small chapter, where we demonstrate the use of audible sound frequencies (<1000 Hz) to direct supramolecular reorganization on an aromatic dipeptide amphiphile. We sought to achieve the formation of larger aggregates as a result of aqueous vibrations, using a variety of spectroscopic (FT-IR, fluorescence, DLS, DOSY NMR) and microscopic techniques (AFM, TEM), investigating the effect of pressure waves on molecular self-assembly.

Resource Type

Doctoral thesis

DOI

10.48730/memq-j054

Date Created

2015

Former identifier

9912517289802996

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Supramolecular systems chemistry using peptides

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