Unfolded, misfolded, and self-organized short alanine-rich peptides: Implications for fundamental science, human disease, and biotechnology

Protein folding is the reversible transition by which an unordered polypeptide chain attains its functional 3-D native structure. A detailed understanding of the principles which govern the protein folding process, such as how sequence codes for structure, remains elusive. Achieving a complete picture of the folding process requires information regarding structural preferences in the unfolded state. Moreover, understanding the principles which govern protein aggregation is of significant biomedical and biotechnological importance. Herein, short alanine-based peptides are used as model systems for studying both the structural preferences in the unfolded state as well as protein aggregation in relation to human disease, and exploitation of the self-assembly process for various biotechnological applications.It is now a central dogma of protein science that the unfolded state is not conformationally random, as was originally believed, but that, instead, residual structure exists. Here, we elucidate the conformational propensities of alanine in the unfolded state using short alanine-rich peptides as model systems. The intrinsic conformational propensities of alanine, as well as nearest neighbor effects are illuminated using various vibrational spectroscopic methods, combined with NMR results.Protein and peptide aggregation is affiliated with various seemingly unrelated diseases, including several neurodegenerative diseases and the systemic amyloidoses. It is of current belief that aggregation is a general feature of the protein energy landscape, suggesting that the various unrelated human pathologies linked to protein aggregation are linked by common principles. Herein, fibril formation of a short alanine-based peptide with no known disease affiliation is probed by vibrational circular dichroism (VCD) spectroscopy. In particular, it is demonstrated that peptide fibrils give rise to VCD intensity enhancement, illustrating the use of the technique as a novel means to probe aggregation kinetics.In addition to the biomedical relevance, protein and peptide self-assembly can be exploited as a means of constructing biomaterials with inherent biofunctionality. In this regard, oligopeptide-based hydrogels have shown potential as drug delivery systems and tissue engineering scaffolds. Herein, the unique properties of a novel class of self-assembling alanine-rich oligopeptides are presented. In particular, it is demonstrated that conformational instability can be exploited to tune the physicochemical properties of hydrogels formed by such systems, for the potential use in various biotechnological applications.