Numerous technological and scientific advancements have been developed by the structural organization and functional capabilities of natural materials. A field known as "biomaterials" focuses on adapting engineering concepts found in biological models to create materials that can solve enduring issues in the biomedical engineering field. The fundamental molecules in a living organism are comprised of proteins. Protein structures are guided by combined and complex intermolecular interactions of peptides which ultimately influence the functionality of proteins. Synthetic engineering approaches of peptides can overcome the limitations of the complexity of protein intermolecular interactions and provide scalable technological solutions. In the current dissertation, an engineering platform called CoOP (co-assembled oppositely charged peptides) was introduced and studied to understand the complex intermolecular interactions of proteins. Inspired by naturally found amyloid-beta (Ab) protein, a hexapeptide framework was designed to determine the effect of pi- stacking, hydrophobic and electrostatic interactions. By using computational and experimental approaches, this unique framework showed the importance of electrostatic interactions to initiate peptide assembly and enhanced stability due to hydrophobic interactions. The usability of this framework was first tested by changing the hydrophobic interactions. Then, assembly kinetics and structural organizations were studied depending on hydrophobicity indexes of amino acids. It was found that the highest hydrophobicity in the framework called [II], formed by co-assembly of KFFIIK and EFFIIE, resulted in the fastest assembly kinetics, showed the most organized secondary structure and similar physical properties as in Ab protein. Given that there is a strong correlation between different aggregated states (fibrillar or globular aggregates) and toxicity of Ab, [II] a platform is provided to study and model these aggregated states. Similar to Ab, oligomeric and fibrillar forms of [II] resulted in a difference in cell membrane damage. However, unlike Ab, [II] platform was implemented to modulate the aggregation where each aggregated state provided different toxicity levels depending on biophysical features. A change in aggregation had control over cell membrane damage, leading to differential and synergistic release of immune system-related molecules. This approach was tested with model antigen Ovalbumin, and antigen-specific antibody production was achieved based on aggregation kinetics. Furthermore, a change of aggregation of [II] was applied to the prophylactic tumor vaccine application, which shows the potential of system for cancer-related applications. Based on the aggregation kinetics, an engineering platform, CoOP, can be applied to correlate structural changes with a biological effect. In this thesis, biological effect is limited based on the applications related to cell membrane damage. However, CoOP provides the discovery of new peptides and functionalities with an understanding of intermolecular interactions.