Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy

Abstract

Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms.

Transient 2D-IR spectroscopy of inorganic excited states

“…Owing to the availability of a number of articles, reviews and, recently, a textbook that discuss the methodology in detail, the intention here is to focus on the spectroscopy and the information content of the data obtained. [11][12][13][14][15] A 2D-IR spectrum is obtained from a 3 rd order nonlinear optical process in which three resonant interactions occur between ultrashort infrared laser pulses and vibrational transitions of the sample. A diagram of the various pulse sequences discussed below is given in Figure 1 where the IR interactions are numbered 1-3 in temporal order.…”

“…In all versions of the 2D-IR experiment, the three interactions lead to the generation of a signal (Sig) by the sample that is then frequency-dispersed and detected via a grating spectrometer, thus providing the 'probe frequency' or 'detection frequency' axis of the spectrum. [11][12][13][14][15] The origin of the 'pump frequency' or 'excitation frequency' axis depends on the experimental methodology employed. The simplest and perhaps most accessible method to non-specialists is the frequency-domain 'double resonance 2D-IR' spectroscopy that uses a tuneable narrow bandwidth pump pulse.…”

“…These off-diagonal peaks arising from vibrational coupling can be applied to decipher spectral contributions in mixtures or to aid spectral assignment. [11][12][13][14][15] In addition, structural information on the studied molecule can be obtained from the 2D-IR spectrum. This is achieved through monitoring the relative amplitudes of diagonal and off-diagonal features with parallel and perpendicular polarization relationships between the pump (denoted 1&2 in Figs 1 and 2) and probe (3) pulses.…”

“…Finally, spectroscopies that provide the ability to correlate vibrational modes in ground and excited states will provide useful information on the molecular changes caused by excitation and the coupling of electronic and vibrational degrees of freedom. One approach to achieving these aims is to extend the multidimensional infrared spectroscopy methods that have found increasing application in the ground state, [11][12][13][14][15] to electronically-excited states. Two-dimensional infrared (2D-IR) spectroscopy, first implemented in 1998, 16 has its basis in the multidimensional NMR experiments that have made major contributions to structural biology research in recent years.…”

“…2D-IR is now employed extensively in the study of ground state systems. [11][12][13][14][15] Exemplars of this include the analysis of offdiagonal peak patterns to determine molecular geometries, 18,19 deconvolute complex spectra 20 or reveal vibrational 21,22 or chemical dynamics, 23,24 while 2D-IR lineshapes report on the fluctuations in a system introduced by interaction with its surroundings, typically nearby solvent molecules. [25][26][27] Crucially, much of this information is either impossible or technologically challenging to extract from 1D experiments.…”