Local Amide I Mode Frequencies and Coupling Constants in Polypeptides

Abstract

Ab initio calculations of the amide I modes of right-handed α -helical, 310-helical, left-handed α -helical, π-helical, parallel β-sheet, antiparallel β-sheet, and fully extended β-sheet polypeptide conformations with two to five peptide bonds were performed to investigate the site dependencies of the local amide I mode frequencies and vibrational coupling constants between neighboring peptides. A Hessian matrix reconstruction method is used to obtain these quantities from the ab initio-calculated amide I normal modes. The local amide I mode frequencies of the peptides in the inner region of a given helical polypeptide are significantly larger than those of terminal peptides, whereas the local amide I mode frequencies of β-sheet polypeptides are not site-dependent. The amide I vibrational coupling constants are not sensitive to the length of the polypeptide, but they are found to be strongly dependent on the three-dimensional conformation of the polypeptides. An empirical model for predicting diagonal amide I mode frequency shift is used to theoretically describe the site dependence of the local amide I mode frequency.

Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Aβ40

“…1B). The non-nearest neighbor interactions along the chains and the nearest neighbor interactions across the chain fixed were fixed at Ϫ1.0 cm Ϫ1 and ϩ1.5 cm Ϫ1 , respectively (34). Because of the isotope shift, the cross-chain coupling did not influence the simulated frequency shifts to any significant extent, thus verifying that the linear-chain spectral concept is robust.…”

“…In Fig. 1B the strands of an ideal ␤-sheet are labeled by s and the carbonyls on a strand are labeled by n. The coupling between the relevant H-bonded amide modes containing the sn and (s Ϯ 1)n carbonyls in adjacent strands of a parallel sheet is generally agreed to be in the range of Ϫ9 to Ϫ11 cm Ϫ1 , while for the next-to-nearest neighbor strands sn and (s Ϯ 2)n the coupling is Ϫ1 to Ϫ2 cm Ϫ1 (34). These results are consistent with a transition dipole-dipole interaction being important in the physical origin of the coupling.…”

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

“…Hessian reconstruction [48] was employed to obtain site frequencies and couplings between the neighboring sites. The magnitude of the CO stretch vibration was used to obtain the eigenvector matrices needed in the reconstruction [50].…”

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.…”

“…11,18,26 In parameterizing the expansion coefficients c i in Eq. (2), generally either the field 12,19,24,26 or the potential 13,14,17,18,25 is chosen to have non-zero coefficients, but not both. The theoretical arguments behind each choice have been discussed in detail by Cho.…”