Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles (original) (raw)
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The Journal of Chemical Physics, 2004
Heterodyned two-dimensional infrared ͑2D IR͒ spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3. Using 1 -13 Cv 18 O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm Ϫ1 , respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm Ϫ1 to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3 peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.
Vibrational spectroscopy, 2006
Over the last 40 years the theoretical basis has been developed for using vibrational spectroscopy as a tool for peptide and protein structure analysis. In spite of these efforts it is still considered to be a low resolution technique, which cannot compete with NMR and X-ray crystallography. However, experimental and computational developments over the last 10 years have provided tools which make vibrational spectroscopy a much more powerful technique. This review focuses mostly, though not exclusively, on the use of the amide I mode for the structure analysis of polypeptides. It evaluates the physical basis of a variety of theoretical and experimental concepts and argues that only a combination of different techniques and spectroscopies can advance the field towards a more precise determination of dihedral angles in even highly heterogeneous polypeptides.
C=O/N Isotope Dependence of the Amide-I/II 2D IR Cross Peaks for the Fully-Extended Peptides
2015
We have used a combination of 2D IR spectroscopy with 13 C= 18 O labeled amide-I and 15 N labeled amide-II modes to reveal how vibrational coupling between labeled peptide units depends on secondary structure. Linear and 2D IR measurements and simulations of C , -diethylglycine homo-tetrapeptide show that this compound adopts the fully-extended (2.05-helical) conformation in CDCl3, consistent with previous work on the Ac-capped peptide. The amide-I/II cross peaks of isotopomers exhibit only a marginal isotope frequency shift between labeled modes that are separated by two peptide units, indicating a very weak coupling. This result is in sharp contrast with a large cross-peak shift observed in 310-helical peptides, in which the labeled amide-I and II modes are connected through an inter-residue C=O•••HN hydrogen bond. The discovered 3D-structural dependence indicates that the 13 C= 18 O/ 15 N labeled amide I/II cross peaks can distinguish the formation of a single 3 10-helical turn from the fully-extended polypeptide chain, and increases the versatility of 2D IR spectroscopy as a conformational analysis tool of biomolecules.
2000
Heterodyned two-dimensional infrared ͑2D IR͒ spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3. Using 1 -13 Cv 18 O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm Ϫ1 , respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm Ϫ1 to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3 peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.
Chemical Physics Letters, 2018
We have combined infrared (IR) experiments with molecular dynamics (MD) simulations in solution at nite temperature to analyse the vibrational signature of the small oppy peptide Alanine-Leucine. IR spectra computed from rstprinciples MD simulations exhibit no distinct dierences between conformational clusters of α-helix or β-sheet-like folds with dierent orientations of the bulky leucine side chain. All computed spectra show two prominent bands, in good agreement with the experiment, that are assigned to the stretch vibrations of the carbonyl and carboxyl group, respectively. Variations in band widths and exact maxima are likely due to small uctuations in the backbone torsion angles.
Chemistry – A European Journal, 2019
Site-specific isotopic labeling of molecules is a widely used approach in IR spectroscopy to resolve local contributions to vibrationalm odes.T he inducedf requency shift of the corresponding IR band depends on the substituted masses, asw ell as on hydrogen bondinga nd vibrational coupling. The impact of these differentf actors was analyzed with ad esigned three-stranded b-sheet peptidea nd by use of selected 13 Ci sotope substitutions at multiple positionsi n the peptide backbone. Single-strand labels give rise to isotopically shiftedb ands at different frequencies,d epending on the specific sites;t his demonstrates sensitivity to the local environment. Cross-strand double-and triple-labeled peptides exhibited two resolved bands that could be uniquely assigned to specific residues, the equilibrium IR spectrao fw hich indicatedo nly weak local-mode coupling. Te mperature-jump IR laser spectroscopy was appliedt o monitors tructural dynamics and revealed an impressive enhancement of the isotope sensitivity to both local positions and coupling between them, relative to that of equilibrium FTIR spectroscopy.S ite-specific relaxation rates were altered upon the introductiono fa dditional cross-strand isotopes. Likewise, the rates for the global b-sheet dynamics were affected in am anner dependent on the distinct relaxation behavior of the labeled oscillator.T his study reveals that isotope labels providen ot only local structural probes, but rather sense the dynamic complexityo ft he molecular environment.
The Journal of Physical Chemistry A, 2013
Vibrational sum-frequency generation (VSFG) spectra of the amide-I band of proteins can give detailed insight into biomolecular processes near membranes. However, interpreting these spectra in terms of the conformation and orientation of a protein can be difficult, especially in the case of complex proteins. Here we present a formalism to calculate the amide-I infrared (IR), Raman, and VSFG spectra based on the protein conformation and orientation distribution. Based on the protein conformation, we set up the amide-I exciton Hamiltonian for the backbone amide modes that generate the linear and nonlinear spectroscopic responses. In this Hamiltonian, we distinguish between nearest-neighbor and non-nearest-neighbor vibrational couplings. To determine nearestneighbor couplings we use an ab initio 6-31G+(d) B3LYP-calculated map of the coupling as a function of the dihedral angles. The other couplings are estimated using the transition-dipole coupling model. The local-mode frequencies of hydrogen-bonded peptide bonds and of peptide bonds to proline residues are red-shifted. To obtain realistic hydrogen-bond shifts we perform a molecular dynamics simulation in which the protein is solvated by water. As a first application, we measure and calculate the amide-I IR, Raman, and VSFG spectra of cholera toxin B subunit docked to a model cell membrane. To deduce the orientation of the protein with respect to the membrane from the VSFG spectra, we compare the experimental and calculated spectral shapes of single-polarization results, rather than comparing the relative amplitudes of VSFG spectra recorded for different polarization conditions for infrared, visible, and sum-frequency light. We find that the intrinsic uncertainty in the interfacial refractive indexessential to determine the overall amplitude of the VSFG spectraprohibits a meaningful comparison of the intensities of the different polarization combinations. In contrast, the spectral shape of most of the VSFG spectra is independent of the details of the interfacial refractive index and provides a reliable way of determining molecular interfacial orientation. Specifically, we find that the symmetry axis of the cholera toxin B subunit is oriented at an angle of 6°± 17°relative to the surface normal of the lipid monolayer, in agreement with 5-fold binding between the toxin's five subunits and the receptor lipids in the membrane.
Vibrational analysis of peptides, polypeptides, and proteins
International Journal of Peptide and …, 1985
The normal modes have been calculated for three kinds of low energy y-turn structures resulting from recent conformational energy calculations by Nkmethy. Frequencies have been computed for a y-turn, a mirror-related 7-turn, and an inverse y-turn of CH3-CO-(L-Ala),-NH-CH3, with n = 3 and n = 5 , and for certain l4 C and l5 N derivatives of the n = 3 molecule. Correlations are evident between amide frequencies and y-turn structures, and it is found that only amide I modes of peptide groups in the turn are relatively insensitive to the lengths of attached chains.
2002
Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band of the small peptide trialanine with that of N-methylacetamide, a commonly used model system for the peptide bond. In contrast to N-methylacetamide, the amide I band of trialanine is significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined with density-functional-theory calculations, the origin of the spectral inhomogeneity is investigated.