Infrared Spectroscopic Studies of Model Biophysical Peptide Systems

Characterization of protein structure is vital to our understanding of biological function and disease progression. While some proteins can be crystallized for structure determination, a vast majority are intrinsically disordered, lacking a well-defined structure. This class of proteins poses a major challenge for developing drugs, as there are limited techniques available to probe drug-target structures in solution. This dissertation sheds light on several infrared spectroscopic methods as promising techniques for studying intrinsically disordered proteins (IDPs) through the use of model peptides. Chapter 3 details insights that can be gained from (1) two-dimensional infrared (2DIR) spectroscopy, focusing on the intracellular neuronal protein, tau, an IDP known be involved in Alzheimer’s disease. Here we utilize backbone isotope labeling and reveal structural organization of toxic aggregated ß-sheets. Chapter 4 introduces (2) visible pump-infrared probe (Vis-IR) spectroscopy and lays the foundation for studying interactions between IDPs and chromophoric inhibitors of amyloid aggregation. Some IDPs undergo a method of liquid-liquid phase separation (LLPS), by which proteins sequester themselves into pockets, or visible droplets, creating two distinct phases within the same solvent. Chapter 5 introduces (3) cysteine cyanylation, a side-chain isotope labeling mechanism, that when combined with 2DIR has the potential to reveal key protein-solvent dynamics driving phase separation. Another area that presents a challenge in unraveling protein structure is the degree to which salts impact protein stability. Recent work has proposed that this effect arises from their direct contact with protein backbone. Chapter 6 introduces N-Methylacetamide, a common model of protein backbone, that in combination with 2DIR spectroscopy, reveals fundamental interactions and proposes structures that can be adopted under specific salt conditions. Chapter 7 expands on N-methylacetamide, utilizing its inhomogeneous nature as an illustration for Fabry-Perot cavity coupling and its use in disentangling quantum information science.