The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure

Abstract

A form of two-dimensional (2D) vibrational spectroscopy, which uses two ultrafast IR laser pulses, is used to examine the structure of a cyclic penta-peptide in solution. Spectrally resolved cross peaks occur in the off-diagonal region of the 2D IR spectrum of the amide I region, analogous to those in 2D NMR spectroscopy. These cross peaks measure the coupling between the different amide groups in the structure. Their intensities and polarizations relate directly to the three-dimensional structure of the peptide. With the help of a model coupling Hamiltonian, supplemented by density functional calculations, the spectra of this penta-peptide can be regenerated from the known solution phase structure. This 2D-IR measurement, with an intrinsic time resolution of less than 1 ps, could be used in all time regimes of interest in biology.The three-dimensional (3D) structure of peptides and proteins and their fluctuations are essential properties responsible for the extremely high specificity of biological reactions. Progress in understanding biological processes such as enzyme reactions originates from the detailed knowledge of the secondary, tertiary, and quarternary structures of the participating biomolecules. Two major spectroscopic techniques are responsible for this development: x-ray scattering, which maps out the electron density of the molecule, and two-dimensional (2D)-NMR spectroscopy (1-3), which can measure the distances between pairs of protons. The next step must be the determination of structures in motion over a wide range of time scales. We believe that multidimensional IR spectroscopy can address this new challenge.The IR spectra of the amide transitions provide information about secondary structural motifs of proteins and peptides. The so-called amide I band, which consists of mostly the stretching motion of the peptide backbone CϭO groups, is a strong IR absorber, which is spectrally isolated from other vibrational modes such as those from amino acid side groups. The amide I states can be viewed as vibrational excitons (4, 5) with the individual peptide groups considered as separated but coupled units. The coupling could be either through-space, such as multipole or even dipole-dipole interaction as proposed by Krimm and Bandekar (4), or through-bond, involving charge shifts and kinematic coupling via the C ␣ atoms of the backbone. The states, which have one excitation present in the whole assembly, can be interrogated by conventional (linear) IR absorption spectroscopy, but the information obtained is insufficient to determine the coupling Hamiltonian, from which a structure might be deduced. More information is available from nonlinear third-order spectroscopic techniques (6) such as the 2D experiment presented here. In a separated system picture both the one-exciton and two-exciton states contribute to the nonlinear IR signal in such a way that all couplings between the separate amide units are available, and in principle a 3D structure of the peptide can be deduced.The success of NMR sp...

Triggered infrared spectroscopy for investigating metalloprotein chemistry

“…Using ultrafast lasers, it has been possible to target coupled vibrational transitions which relax within picoseconds. This was applied by Hamm et al (1999) to analyse through-space or through-bond coupling between amide I bands of peptide units in a small cyclic pentapeptide for which all amide I transitions could be resolved in the spectrum, to obtain structure-dependent information. Extension to larger peptides and proteins is much more difficult because of overlapping amide I bands which cannot be assigned to specific residues, but the approach may have exciting applications for distance/structure determination within proteins or for pairs of interacting proteins that have been labelled with vibrationally active probes at strategic locations.…”

“…The exact shape and position of these bands vary with the secondary protein structure and the presence of hydrogen-bonding interactions. For very small oligopeptides, it is sometimes possible to assign individual amide I bands to specific peptide C=O units (Hamm et al 1999), but for most proteins, the amide bands represent a superposition of the vibrational bands arising from each residue and thus report only on global structure in the protein, in particular, the extent of a-helix, b-sheet or random coil. This article focuses particularly on the possibilities arising from recent IR technical developments for studies that monitor identifiable, localized vibrational oscillators in proteins (figure 1).…”

Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

“…9 Although simple in form, the accurate structure-based parameterization of this Hamiltonian is non-trivial and has been the subject of numerous computational studies. [11][12][13][14][15][16][17][18][19][22][23][24][25][26] Siteto-site coupling constants are generally extracted by a combination of electrostatic models (e.g., dipole-dipole 22,27 or transition charge coupling 11,13,15,28 ) and DFT-parameterized dihedral maps for nearest-neighbor interactions. 11,13,18,22,26 Site energy maps are based on the observation that electrostatic interactions (particularly hydrogen bonding) between a solvated molecule and its environment are the primary predictors of local vibrational frequencies.…”

Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids

“…28 This upper limit is smaller than the observed rms value of 46 cm −1 , which suggests that the coupling between the neighboring OH groups in liquid methanol may involve additional mechanisms besides transition-dipole coupling, for instance, hydrogen-bond mediated coupling. 12,13,25 The information obtained from the simultaneous absorption spectrum is to some extent comparable to that derived from two-dimensional optical spectroscopy methods, [29][30][31] which can also be used to determine couplings between vibrations 14,32,33 and correlations between vibrational fre- quencies. However, two-dimensional vibrational spectroscopy requires that the coupled vibrations have different center frequencies, whereas simultaneous absorption, like the Raman noncoincidence effect, 17,18,20,21 can also provide information on interacting vibrations having the same center frequency.…”

“…We treat the coupling as a perturbation, denoting by ͉ij͘ the unperturbed state having the OH-stretch mode of molecule A in the v = i vibrational level, and the OH-stretch mode of neighboring molecule B in the v = j vibrational level. Using harmonic approximations for the wave functions, 14,15 we have ͗11͉q 1 q 2 ͉11͘ = 0, so that the first-order correction to the energy of the simultaneously excited state ͉11͘ vanishes. 15 The second-order energy correction with respect to the situation without coupling is given by 16 …”