The self-assembly of proteins and peptides into complex supramolecular structures provides an important avenue in the development of materials for biomedical applications. In particular, the design and fabrication of protein and peptide-based hydrogels has emerged as an attractive route toward novel materials with tunable three-dimensional chemical and physical structure, biodegradability, biocompatibility, as well as drug loading and release properties. These unique characteristics offer great potential for the utilisation of self-assembled hydrogels as drug delivery vehicles, biomedical materials, and tissue engineering scaffolds. A class of materials highly suitable for such applications due to their biodegradability and lack of cellular toxicity is silk-derived proteins. Regenerated silk fibroin (RSF) in particular, retains most of the properties of native silk but is readily available through scalable processes. This natural block copolymer has the propensity to self-assemble into a fibrillar network that is β-sheet rich, and its biocompatibility coupled with its remarkable mechanical properties make this protein an excellent candidate as a material for biomedical applications.

A facile and reproducible route towards the fabrication of novel materials, featuring organised and multicompartmental structure with high particle monodispersity can be achieved through microfluidics, and in particular, droplet-based approaches. In this thesis, microfluidic techniques are employed to generate microcapsules comprised of a protein-fibrillar network. Capsules exhibiting complex internal structure were fabricated, while droplets ranging from hundreds of nanometers up to hundreds of microns, were generated. Furthermore, different approaches as to how such microcapsules/microgels can be used for biomedical applications are presented through the generation of hierarchical emulsions, but also through the formation of Janus-like microgels, exhibiting enhanced release kinetic profiles.

Furthermore, by integrating silver nanoparticles with silk-based microcapsules, I was able to systematically form organic/inorganic microgels, and investigate their properties both in vitro and in vivo. Not only did these hybrid microgels display potent antimicrobial properties, but in contrast to conventional treatments involving silver, the organic/inorganic microgels showed minimal cytotoxicity towards mammalian cells, making them ideal for wound healing purposes. To this effect, the antibacterial and wound healing properties of the hybrid microgels were investigated through the use of a murine model. It was determined that the efficacy of this system is comparable to results obtained when using a conventional antibiotic such as ampicillin, which clearly demonstrates the potential of the hybrid microgels for treatment of surgical site infections.

The successful delivery of cargo molecules for cell related applications mostly depends on particle size and its distribution. Although traditional methods of generating nanoparticles have resulted in significant advances, some of which are currently used for pharmaceutical treatments, systematic control over size and monodispersity remains challenging. In order to address this issue, I developed a microfluidic/nanofluidic device capable of generating nanosized water-in-oil emulsions, with sizes ranging from 2500 down to 50 nm. By adding monomeric protein to the aqueous phase, these nanoemulsions acted as templates to form nanogels, which had the ability to permeate through mammalian cancer cell membranes and deliver intracellular cargo.

Finally, in order to gain a better understanding of the processes involved in protein self-assembly, novel label-free approaches which utilise the fluorescence of the intrinsic amino acid, tryptophan, were investigated. It was found that during protein self-assembly, or more generally during protein phase transitions which involve hydrophobic burial, an increase in the tryptophan fluorescence signal was observed. This allowed for a systematic study of protein phase transitions, such as fibril, spherulite and crystal formation, without resorting to extrinsic fluorophores, paving the way for a label-free method to monitoring self-assembly events. In order to fully explore the potential of observing such events in a massively parallel way, I developed a microfluidic device capable of trapping thousands of individual droplets under zero-flow conditions. This device was used to spatially confine and temporally monitor biomolecular interactions within thousands of droplets simultaneously, and the statistical character of self-assembly could thus be highlighted.