Examining peptide and protein structure and dynamics with two-dimensional infrared spectroscopy

Abstract

Knowledge of peptide and protein structure is critical for understanding how they carry out their biological roles. In this dissertation, I describe how two-dimensional infrared (2D IR) spectroscopy coupled with isotope labeling can capture detailed molecular changes in polypeptides. I have investigated how isotopes can detect local structural changes within a model alpha-helix, which represent the largest class of protein secondary structures. In this study, isotope-edited vibrational signatures revealed hydrogen bonding and vibrational coupling between the probes at the helical turns, providing an enhanced way to detect alpha-helical folding and unfolding. I have also demonstrated how this nonlinear technique can monitor polypeptide features in the presence of certain nanoparticles, which are becoming increasingly prevalent in our society. Lastly, I implemented this technique to characterize the influenza A M2 proton channel, a transmembrane alpha-helical peptide that is essential for viral replication. A characteristic vibrational mode was detected and assigned to the highly-conserved His37-tetrad, which is an exquisitely selective region for proton conduction. Additionally, time-dependent isotopic features at positions Val27, Ala30, and Gly34 revealed lineshape changes, indicative of ultrafast (subpicosecond) water dynamics in the channel. In summary, this dissertation describes how 2D IR spectroscopy and isotope labeling methods can elucidate molecular changes within various polypeptides, which can be expanded to probe the structures and kinetics of more complex biomolecular systems.