Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics
ABSTRACT We have developed a Fourier transform two-dimensional infrared (2D IR) spectrometer to probe chemical reactions and biophysical processes triggered by a nanosecond temperature jump (T jump). The technical challenges for such a spectrometer involve (1) synchronization of a nanosecond T-jump laser and femtosecond laser system, (2) overcoming the decreased signal-to-noise ratio from low repetition rate data acquisition, and (3) performing an interferometric measurement through a sample with a density and index of refraction that varies with time delay after the T jump. The first challenge was overcome by synchronizing the two lasers to a clock derived from the Ti:sapphire oscillator, leading to timing accuracy of 2 ns for delays up to 50 ms. The data collection time is reduced by using undersampling with the improved signal-to-noise ratio obtained from a balanced detection scheme with a dual stripe array detector. Transient dispersed vibrational echo and 2D IR spectroscopy are applied to N-methylacetamide and ubiquitin, as examples, and the spectral responses by a temperature elevation and by structural changes of the protein are compared. The synchronization of 2D IR spectroscopy with a nanosecond temperature jump without losing its sensitivity at a low repetition rate opens a new applicability of the nonlinear spectroscopy to probe a variety of molecular structure changes induced by a nanosecond perturbation.
- SourceAvailable from: Ziad Ganim[Show abstract] [Hide abstract]
ABSTRACT: Transient two-dimensional infrared (2D IR) spectroscopy is used as a probe of protein unfolding dynamics in a direct comparison of fast unfolding experiments with molecular dynamics simulations. In the experiments, the unfolding of ubiquitin is initiated by a laser temperature jump, and protein structural evolution from nanoseconds to milliseconds is probed using amide I 2D IR spectroscopy. The temperature jump prepares a subensemble near the unfolding transition state, leading to quasi-barrierless unfolding (the "burst phase") before the millisecond activated unfolding kinetics. The burst phase unfolding of ubiquitin is characterized by a loss of the coupling between vibrations of the beta-sheet, a process that manifests itself in the 2D IR spectrum as a frequency blue-shift and intensity decrease of the diagonal and cross-peaks of the sheet's two IR active modes. As the sheet unfolds, increased fluctuations and solvent exposure of the beta-sheet amide groups are also characterized by increases in homogeneous linewidth. Experimental spectra are compared with 2D IR spectra calculated from the time-evolving structures in a molecular dynamics simulation of ubiquitin unfolding. Unfolding is described as a sequential unfolding of strands in ubiquitin's beta-sheet, using two collective coordinates of the sheet: (i) the native interstrand contacts between adjacent beta-strands I and II and (ii) the remaining beta-strand contacts within the sheet. The methods used illustrate the general principles by which 2D IR spectroscopy can be used for detailed dynamical comparisons of experiment and simulation.Proceedings of the National Academy of Sciences 10/2007; 104(36):14237-42. DOI:10.1073/pnas.0700959104 · 9.81 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: We present a detailed discussion of the complimentary fields of the application of two-dimensional infrared (2D-IR) spectroscopy in comparison with two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy. Transient 2D-IR (T2D-IR) spectroscopy of nonequilibrium ensembles is probably one of the most promising strengths of 2D-IR spectroscopy, as the possibilities of 2D-NMR spectroscopy are limited in this regime. T2D-IR spectroscopy uniquely combines ultrafast time resolution with microscopic structural resolution. In this article we summarize our recent efforts to investigate the ultrafast structural dynamics of small peptides, such as the unfolding of peptide secondary structure motifs. The work requires two ingredients: 2D-IR spectroscopy and the possibility of triggering a structural transition of a peptide on an ultrafast timescale using embedded or intrinsic photoswitches. Several photoswitches have been tested, and we discuss our progress in merging these two pathways of research.Annual Review of Physical Chemistry 02/2008; 59:291-317. DOI:10.1146/annurev.physchem.59.032607.093757 · 15.68 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: We review two-dimensional infrared (2D IR) spectroscopy of the amide I protein backbone vibration. Amide I modes are known for secondary structural sensitivity derived from their protein-wide delocalization. However, amide I FTIR spectra often display little variation for different proteins due to the broad and featureless line shape that arises from different structural motifs. 2D IR offers increased structural resolution by spreading the spectra over a second frequency dimension to reveal two-dimensional line shapes and cross-peaks. In addition, it carries picosecond time resolution, making it an excellent choice for understanding protein dynamics. In 2D IR spectra, cross peaks arise from anharmonic coupling between vibrations. For example, the spectra of ordered antiparallel beta sheets shows a cross peak between the strong nu perpendicular mode at approximately 1620 cm(-1) and the weaker nu parallel mode at approximately 1680 cm(-1). In proteins with beta-sheet content, disorder spreads the cross peaks into ridges, which gives rise to a "Z"-shaped contour profile. 2D IR spectra of alpha helices show a flattened "figure-8" line shape, and random coils give rise to unstructured, diagonally elongated bands. A distinguishing quality of 2D IR is the availability of accurate structure-based models to calculate spectra from atomistic structures and MD simulations. The amide I region is relatively isolated from other protein vibrations, which allows the spectra to be described by coupled anharmonic local amide I vibrations at each peptide unit. One of the most exciting applications of 2D IR is to study protein unfolding dynamics. While 2D IR has been used to study equilibrium structural changes, it has the time resolution to probe all changes resulting from photoinitiated dynamics. Transient 2D IR has been used to probe downhill protein unfolding and hydrogen bond dynamics in peptides. Because 2D IR spectra can be calculated from folding MD simulations, opportunities arise for making rigorous connections. By introduction of isotope labels, amide I 2D IR spectra can probe site-specific structure with picosecond time resolution. This has been used to reveal local information about picosecond fluctuations and disorder in beta hairpins and peptides. Multimode 2D IR spectroscopy has been used to correlate the structure sensitivity of amide I with amide II to report on solvent accessibility and structural stability in proteins.Accounts of Chemical Research 04/2008; 41(3):432-41. DOI:10.1021/ar700188n · 24.35 Impact Factor