Signatures of β-Peptide Unfolding in Two-Dimensional Vibrational Echo Spectroscopy: A Simulation Study

295

291

The power of two-dimensional (2D) IR spectroscopy as a structural method with unprecedented time resolution is greatly improved by the introduction of IR polarization conditions that completely eliminate diagonal peaks from the spectra and leave only the crosspeaks needed for structure determination. This approach represents a key step forward in the applications of 2D IR to proteins, peptides, and other complex molecules where crosspeaks are often obscured by diagonal peaks. The technique is verified on the model compound 1,3-cyclohexanedione and subsequently used to clarify the distribution of structures that the acetylproline-NH 2 dipeptide adopts in chloroform. In both cases, crosspeaks are revealed that were not observed before, which, in the case of the dipeptide, has led to additional information about the structure of the amino group end of the peptide.H eterodyned 2D IR experiments have recently been reported that are the IR analogues of pulsed correlated spectroscopy and nuclear Overhauser effect spectroscopy in 2D NMR (1-5). Like 2D NMR spectra that exhibit diagonal peaks at frequencies determined by one-dimensional spectra and crosspeaks between coupled nuclear spins, 2D IR spectra contain diagonal peaks and crosspeaks that represent coupled vibrational transitions. The 2D IR crosspeak intensities and splittings depend on the angles and distances between the vibrational modes and can be used to characterize the structures of peptides (3, 6, 7). One advantage (8) of 2D IR over other structure-determining methods is the time scale; 2D IR can monitor structures on a picosecond timescale, which allows transient protein dynamics to be followed. However, structural information is lost when the crosspeaks overlap with the more intense diagonal peaks. Methods have been developed in 2D NMR to minimize the overlap of diagonal and crosspeaks (9, 10). Here we report a technique based on quite different principles that completely eliminates the diagonal peaks from 2D IR spectra and allows the crosspeaks and hence structures to be more easily and better characterized.A useful characteristic of IR transitions is that the directions of their transition dipoles in the molecular frame are often predictable. For example, modes that are mainly localized on two atoms such as NOH, COH, or CAO stretches usually have transition dipole vectors near the bond axis, and the amide I modes of peptide units have transition dipoles whose directions are given by the positions of the amide atoms (11). The four polarized IR pulses in the 2D IR experiments successively interact with four transition dipoles of each molecule, and thus polarized 2D IR measurements can yield information on the geometric arrangements of the dipoles. The diagonal peaks are generated when the IR pulses all interact with the same mode and therefore interrogate only a single location in the structure. The crosspeaks are generated when the IR pulses interact with modes in different locations. The results are couplings and relative orientations that can be used t...

Section: H Eterodyned 2d Ir Experiments Have Recently Been Reportedmentioning

confidence: 99%

Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination

Zanni

Kim

et al. 2001

295

291

“…High-level ab initio methods are too expensive for peptides larger than 10-15 units, especially when the Hamiltonian must be parameterized at many steps along a molecular dynamics trajectory (26)(27)(28). For this reason, recent studies of amide modes in large peptides have turned to approximations such as electrostatic coupling (1,2,5,19,25,27,29) or the use of maps based on ab initio calculations for smaller units (4,24,26,30,31) to compute coupling constants.…”

mentioning

confidence: 99%

The origin of vibrational mode couplings in various secondary structural motifs of polypeptides

Moran

Mukamel

2004

109

135

Electrostatic (through-space) and covalent (through-bond) contributions to couplings involving the CAO and CON vibrational stretching modes of the amide group in the ␣-helix and the parallel and antiparallel ␤-sheet structures of alanine polypeptides are analyzed. Coupling constants computed at the density functional theory level are compared with the transition dipole coupling model and the complete electrostatic interaction between transition densities. We find that the transition densities of CAO modes are localized, and the electrostatic mechanism then holds. In contrast, the CON mode transition densities are delocalized, and covalent contributions to the coupling are significant.

“…Furthermore, the methods allow the determination of key parameters of the anharmonic potential surfaces of peptides and hence provide important tests of theoretical calculations of molecular structure and dynamics (8,9). These coherent nonlinear IR techniques permit experimental determination of the coupling and angular relations of vibrators by using experimental protocols that are analogous to those developed for NMR.…”

mentioning

confidence: 99%

Dual-frequency 2D-IR spectroscopy heterodyned photon echo of the peptide bond

Rubtsov

Wang

Hochstrasser

2003

149

161

The structure fluctuations of the peptide bond interacting with solvent are examined through the coupling and correlations of the frequency distributions of amide I and amide II transitions. The fluctuations of the two modes are anticorrelated as a result of the solvent-induced changes in the mixing of the dominant valence-bond structures of the peptide. Significant anharmonic coupling of the two modes is seen. The results are the application of a new approach to two-dimensional infrared (2D-IR) spectroscopy in which the pulse sequences used to produce the vibrational echoes incorporate two frequencies. This dual-frequency arrangement greatly extends the capabilities of 2D-IR spectroscopy by allowing the coupling between widely separated modes to be characterized in analogy with heteronuclear NMR. The experiment exposes the cross peaks, representing the mode coupling, free of the interference of the strong diagonal peaks that typically dominate 2D-IR spectroscopy. The alignment and dephasing of coupled transitions, in this example the amide I and amide II transition dipoles, is also determined by these experiments.M ultidimensional IR spectroscopy, in particular 2D-IR spectroscopy, is a powerful new method with which to obtain the time dependence of structural features of complex molecular systems, including peptides and proteins, under ambient conditions in solutions (1-7). Furthermore, the methods allow the determination of key parameters of the anharmonic potential surfaces of peptides and hence provide important tests of theoretical calculations of molecular structure and dynamics (8, 9). These coherent nonlinear IR techniques permit experimental determination of the coupling and angular relations of vibrators by using experimental protocols that are analogous to those developed for NMR. The first such experiments concerned the amide I modes of peptides, which are mainly CAO vibrators (1)(2)(3)(4)(5)(10)(11)(12). In such cases all of the relevant frequencies of an interacting ensemble of modes could readily be bracketed by the spectral bandwidth of 120-fs IR laser pulses. The response of such a system to sequences of three pulses, each with the same center frequency in the amide I region, gave rise to coherent signals, the 2D and 3D correlation spectra of which yielded the relevant structural and dynamical information. In a recent advance, 2D-IR spectroscopy experiments incorporating two pulses with different frequencies, one in the NOH and the other in the amide I region of peptides, were successful in measuring the coupling and angular relations between NOH and CAO modes in some simple peptides (13)(14)(15).In this article we report a dual-frequency 2D-IR spectroscopy heterodyned photon-echo experiment. The 2D-IR spectra, which require manipulation of the vibrational coherences by the interaction of short laser pulses with inhomogeneously broadened distributions of transition frequencies, consist of diagonal features and cross peaks. The diagonal peaks are independent properties of each of the anharmonic m...