Use of bioinspired, genetically engineered proteins in tissue engineering scaffolds represents a new opportunity for engineering these constructs. However, the production and rational modification of new, artificial proteins is hindered by significant gaps in knowledge regarding expression of artificial gene constructs in E. coli and their molecular modeling. This thesis focuses on the production of a novel hydrogel scaffold composed of four self-assembling protein modules and their rational modification using Molecular Dynamics (MD) simulations. Two of the modules are based on the ABA triblock copolymer design. In this triblock, a hydrophilic, random coiled region is flanked by 28 amino-acid α−helical endblocks. The purpose of these endblocks is to function as virtual crosslinkers and support network formation. The length of the endblocks can be changed by the addition of two unlinked, fiber-forming peptides and thus potentially alter the gelation and melting points of the hydrogel. We evaluate the efficacy of production of these endblocks by two separate expression strategies in E. coli and demonstrate their ability to form hydrogels. Furthermore, we analyze the Gibbs free energy of formation of oligomeric intermediates that arise early on during fibrillogenesis from the unlinked peptides using the MM/PBSA module of Amber 9. Thermodynamic data demonstrates changes in the primary structure of these peptides affect the stability of the intermediate that seeds fiber formation. This analysis also suggests a shift in the fiber forming mechanism from monomer addition to protofibril addition. We offer how this data can be used to improve interhelical interactions between endblocks and unlinked peptides and how to develop coarse-grain models of fiber formation.