Natural filamentous shaped biomolecules utilize their physical shape and chemical functionality to optimize and achieve hierarchical structures. They use weak interaction such as hydrogen bonds, hydrophobic interaction, charge-charge interaction, van der Waals force and so on. The major advantage of using weak interactions is that they enable biomolecules to adopt the reversible assembly and reorganization of the structures. In my work, I use M13 bacteriophage (M13 phage) to investigate how intrinsic molecular interaction affect phase transition, self-assembly process, and hierarchical structure formation. I used genetically engineered phage with the peptide motif of elastin-like polypeptide (ELP). Insertion of target sequence of peptide on the surface of M13 phage can endow functionality on the M13 phage. Firstly, I investigated novel liquid crystalline transition upon stimuli application. Counterintuitive liquid crystalline order increase upon heating was investigated with engineered M13 phage. Secondly, molecular crowding environment make M13 phage forming long-range ordered smectic structures. The addition of non-interacting colloidal particles provides depletion force to phage and accelerate their assembly. Due to the intrinsic molecular interaction engineered phage, I investigated time dependent structure evolution process. Last, I applied ELP as interacting colloids to engineered phage. Because ELP possesses same peptide motif, they could have interaction despite different molecular shape. Unlike the mixture system of phage and non-interacting colloids, engineered phage and ELP mixture system showed dual phase transition and helical fiber formation. Furthermore, I could turn off and on the depletion force by controlling temperature. I show that our novel liquid crystalline phase transition is based on the attractive interaction. Through my dissertation, I hope the combination of functionality of peptide and liquid crystal molecule could convey the insight for molecular design and development of hierarchical structure formation.

Bioelectricity is generated by a wide spectrum of living organisms, ranging from single-celled entities to intricate multicellular organisms. These organisms have evolved intricate mechanisms to regulate and manage electrical activity. The understanding and controlling of bioelectricity hold the potential to yield diverse bioelectrical applications. However, comprehending bioelectrical systems using conventional organic/inorganic materials remains challenging because these materials lack the inherent complexity and adaptability that make replication difficult, limiting their capacity for modification and customization. Biological systems are highly complex, comprising various components such as nucleic acids, proteins, and tissues that display high specificity and selectivity in their interactions and processes. This complexity and heterogeneity hinder the accurate replication or mimicry of biological processes at the molecular level. Viruses, being submicroscopic infectious entities, serve as powerful tools for advancing our understanding of fundamental biological systems. Using the M13 phage as a model system due to its simple structure, versatile, biocompatible, and massively replicable characteristics, the structure-function relationship of bioelectricity is studied. This thesis explores the responsive electrical properties of viruses to external stimuli such as friction, mechanical stress, heat, and chemical environments. It examines how genetic modifications of viruses alter their structural and electrical properties, introducing practical virus-based bioelectrical applications. By using the M13 phage as a model system for investigating bioelectricity, this research aims to offer valuable insights into the design and development of innovative bioelectrical applications, bridging the gap between conventional materials and biological systems.

Smart biomaterials that can actively respond to and interact with their environment are sought after for regenerative medicine, therapeutic delivery, sensing, and actuation. Polymer-nanoparticle hybrids are a promising class of smart materials, but thus far the choice of polymers has predominantly been chemically synthesized ones. In contrast, natural tissues commonly utilize proteins to interface with nanoparticles and provide smart functionalities. Inspired by nature, this dissertation describes the development of genetically engineered, protein-based polymers (PBPs) for use as components of smart, polymer-nanoparticle hybrids. Specifically, elastin-like polypeptides (ELPs), a class of thermoresponsive PBPs, were utilized to functionalize two nanoparticles.

First, an improved method for synthesizing PBP genes was developed. Crafting new PBPs is limited by the ease with which their genes can be engineered. The new method utilizes a specific architecture of restriction enzymes to address some of the drawbacks of previous methods and was used to efficiently and accurately produce ELP genes.

Next, ELPs were engineered to display biomimetic, bone mineral-binding peptides and their effect on therapeutic bone cements was investigated. Bones are mechanically robust, composites composed predominantly of proteins and nanocrystalline mineral. In contrast, bone cements are brittle and do not contain organic materials. Composites of mineral-binding ELPs and cement had significantly improved strength. Furthermore, the injectability and washout resistance of cements were improved as a result of the ELP's thermoresponsive behavior.

Finally, photoresponsive composites were created by engineering ELPs to display graphene-binding peptides. Graphene-derived nanoparticles (GNs) exhibit unique mechanical, electrical, and optical properties but are difficult to integrate into biological systems due to their hydrophobic nature. The engineered ELPs non-covalently bound to GNs and the resulting ELP-GN hybrids exhibited increased colloidal stability and a reversible temperature-controlled aggregation behavior. The ability of GNs to convert near-infrared light to heat was exploited in order to remotely induce aggregation of ELP-GN hybrids in solution and to induce rapid, site-specific actuation of ELP-GN composite hydrogels. Finally, cell adhesion on ELP-functionalized graphene was enhanced by genetic addition of integrin-binding peptide motifs.

These studies demonstrate that PBPs can be tailored to interact with nanoparticles of choice and can provide stimuli-responsive and bioactive properties to biologically relevant nanoparticles. Hybrid materials of PBPs and nanoparticles are, therefore, well suited for biotechnological applications which require smart behavior.

Hydrogels have been used to develop scaffolds to address challenges in tissue engineering and drug delivery for several decades. The major advantage of using hydrogels is that their high water content and low stiffness enables them to mimic tissue-like environments. In my work, I develop four unique hydrogels using a single polymer, elastin-like polypeptide. The first challenge I address is that of hydrogel extensibility. Typical hydrogels cannot undergo large strains, which limits their durability and applicability to active tissues such as muscles. I use ELP to create a rubber-like elastic hydrogel that can stretch to 15 times its original length. Unlike most previous ELP hydrogels, our gels can reach such high strains due to the well-defined structure of our materials with minimal crosslinks. Next, I focus on developing an adhesive hydrogel using ELP. Unlike most adhesives, especially protein-based adhesives, our adhesive hydrogels are flexible and deswell in physiological conditions. This improves their potential for success in practical applications. We also developed a self-healing hydrogel by combining ELP with bioglass. Unlike other strategies that use reversible physical bonds, we use pH driven reversible Schiff base formation to synthesize hydrogels. Bioglass raises the localized pH to yield ideal conditions that favor gelling in our system. We also show that our materials can self-heal after being severed, which makes them durable and ideal for topical applications. Finally, we employ our efforts in the design and synthesis of protein-based beads for biolaser development. These devices are stimuli-responsive, which makes them ideal for optical sensing applications for biomolecule sensing and the flexibility of the hydrogels also makes them suitable for studying cellular biophysics. Through my dissertation, I hope to convey the versatility of ELP and the potential of structural design that can lead to the development of hydrogels with diverse functions.