ABSTRACT
Multimode Amide I/II 2D IR Spectroscopy ............................................................ 394 12.5.3 Transient T-Jump Spectroscopy as a Probe of Unfolding Dynamics of TrpZip2 ..... 395
12.5.3.1 Transient 2D IR: Nanosecond Response ................................................... 397 12.5.3.2 Transient 2D IR: Microsecond Response .................................................. 397 12.5.3.3 Assignment of Markov States .................................................................... 397
Proteins are molecules that behave in beautiful and astounding ways in the course of their biological function, and all biological processes involve protein conformational changes. These processes might be enzyme catalysis, transport and signaling, dynamic scaffolding for structures, charge transfer, or mechanical or electrical energy transduction. Our view of such processes is colored by the methods we use to study them, and most of what we know about proteins is based on structural studies and biochemical assays. Biochemists and biologists think of the processes in which proteins engage in terms of directed motion, often illustrating them through movies, but in current experiments, one rarely actually watches the conformational changes that occur directly. The method of two-dimensional infrared (2D IR) spectroscopy [1-3] is providing new approaches that can be used to characterize the features that are masked by traditional methods, particularly for visualizing conformational dynamics on picosecond to millisecond timescales, and characterizing the conformational variation and structural disorder. Furthermore, it is also proving useful for samples that are difcult to study by traditional techniques, such as protein aggregates and amyloid bers [4,5], intrinsically disordered peptides [6], and membrane proteins [7,8].
