| Understanding the rules of self-assembly in a large-scale biological structure is crucial to the design and fabrication of functional nanostructured materials. Substantial research efforts have made it possible to identify the elements that are important in stabilizing the highly complex quaternary structures of several proteins, including viral capsids, several types of intra and extracellular matrices and a group of disease-related polypeptides/proteins exhibiting a "cross-beta" sheet structure. This thesis describes the de novo design of synthetic mimetics of two protein motifs, alpha-helical coiled coils and amyloid beta-sheets and the parameters which control conversion between these two motifs. Chapter 1 reviews the current progress of self-assembled synthetic polypeptide based nanofibrous materials. Chapter 2 investigates the pH-dependent helical stability of de novo designed short coiled coil homodimers and heterodimers. Chapter 3 discusses the general problem of the lateral aggregation seen in most of the coiled coil based nanofiber systems. In addition, the concentration-dependent fiber formation has been generalized as an intrinsic property of peptides with similar primary sequences. In chapter 4, the dynamic secondary structure of coiled coil-sequenced peptides has been extensively studied using a variety of biophysical methods including CD, ATR FT-IR, grazing angle FT-IR, TEM, cryo-TEM, and AUC. The secondary structure helix-sheet transition with the commensurate amyloid formation was found to be associated with the presence of the hydrophobic clusters in the central region of the primary sequence, which leads to the aggregation of the individual beta-sheet into a sandwich-like assembly. In chapter 5, utilizing the understanding of hydrophobic clusters gained in chapter 4, a new class of fiber-forming multidomain peptide (MDP) was developed with an alternating pattern of hydrophobic and hydrophilic residues. Controlled nanostructural morphology, in this case soluble nanofibers with controlled length, was achieved by varying the ratio of the central repeating number of (Gln-Leu) and the flanking charged lysine residues. Finally, chapter 6 discusses the application of the MDP in 3-D cell culture as an extracellular matrix mimetics. The attachment of short peptide sequences (RGDS and PHSRN) was found to dramatically enhance the cell proliferation rate. The fact that the biological active motifs can be specifically recognized on these peptide-based scaffolds will encourage further investigation of attaching diverse biologically functional constructs on these peptide matrices for specific tissue repair and regeneration. |
