Using 2D IR Spectroscopy to Examine Biomolecular Structures, Dynamics, and Mechanisms
Ultrafast two-dimensional infrared (2D IR) spectroscopy uses a series of femtosecond mid-IR laser pulses to provide near-instantaneous “snapshots” of vibrational ensembles. 2D IR spectra provide detailed information about the frequencies of vibrational modes and coupling between them, and the femtosecond-picosecond timescale resolution of the technique provides a direct probe of short timescale dynamics. My group uses 2D IR spectroscopy to address a variety of problems in biochemistry and biophysics at the intersection of structure, dynamics, and mechanism. In my talk, I will give a brief overview of the information content of 2D IR spectra and will present my group’s recent work in three areas. First, I will discuss our work on the membrane-dependent aggregation of the C-terminal peptide of the pro-apoptotic human protein Bax (“a9p”), which – contrary to previous reports – forms amyloid aggregates in solution and on lipid bilayers via a mechanism bearing a strong resemblance to disease-related amyloids (e.g., Ab). These results (and others) suggest a possible amyloid pathway in apoptosis. Second, I will discuss how we used 2D IR spectroscopy and isotope labeling to define the K+-dependent assembly landscape of four-stranded DNA motifs known as G-quadruplexes, the order of K+ binding to specific sites within them, and how their assembly under different conditions influences the sensitivity of a common G-quadruplex binding fluorophore (thioflavin T). I will also show how we used empirical measures of vibrational coupling effects to determine the first (to our knowledge) “all IR” structure of a DNA G-quadruplex. Finally, I will discuss how we employed a modular vibrationally labeled substrate analog to probe femtosecond-picosecond solvation dynamics in the active site of a promiscuous hydride/proton transfer enzyme, as well as the imprint of solvation on the substrate analog’s intramolecular vibrational dynamics. These results show a complex interplay between system/bath dynamics that diverges between various substrate binding modes and may impact the mechanism(s) of hydride/proton transfers. During my presentation, I will highlight emergent hypotheses as well as ongoing studies in each of these areas of research.
Hosted by Professor Lu Wang
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