Ultrafast 2D IR spectroscopy of membrane peptide systems




Flanagan, Jennifer Catherine

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Plasma membranes are the main liaisons between the intercellular and extracellular environment, playing a critical role in numerous biological processes. Recent research has challenged the long-standing "fluid mosaic model," representing membranes as densely packed, heterogeneous environments. Within these complex membranes are transmembrane proteins which comprise up to 50% of the membrane mass, and are themselves diverse in sequence, structure, and function. Combining two-dimensional infrared spectroscopy (2D IR) and molecular dynamics simulation (MD), this thesis explores membrane complexity from two perspectives: first, it addresses the sequence heterogeneity in transmembrane peptides; and second, it explores the effect this crowded environment has on the lipids themselves and the implications this has on future membrane studies. Site-specific hydration of transmembrane peptides was probed using singly isotope-labeled pH (Low) Insertion Peptides, or pHLIPs. These peptides are a class of small transmembrane helices containing ~30% polar residues. By including a single-residue ¹³C=¹⁸O isotope label on the pHLIP backbone, IR experiments effectively produce a single-residue spectrum separate from the main peptide peak. With computational models to connect atomistic structure from MD to infrared frequency shifts, these site-specific spectra reveal local hydration as far as 1 nm into the hydrophobic membrane core. Crowding experiments probed dynamics at the lipid-water interface of model membranes as a function of transmembrane peptide concentration. These dynamics, drawn from time-dependent 2D IR, trend non-monotonically with peptide concentration, revealing three dynamical regimes: a pure lipid-like, a bulk-like, and a crowded regime. Through similar computational methods, these dynamics were linked to water structure at the lipid-water interface, which is perturbed by peptide insertion. Finally, preliminary work has been carried out in developing transient 2D IR methods for applications to protein folding. The first pH-jump 2D IR experiment has been performed by implementing an ultraviolet pump laser to a photoacid-containing sample. Pumping the sample with UV dissociates the photoacid, causing an instantaneous, local pH drop, and the effect on the sample is probed by 2D IR. This new method extends the picosecond-scale 2D IR experiment to a micro-to-millisecond timescale, and has potential for studying pH-initiated conformational transitions such as protein folding and polymerization.



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