Conformational analysis of tetrapeptides by exploiting the excitonic coupling between amide I modes

Abstract

The amide I band of the IR and to a lesser extent also of the corresponding visible Raman spectra of peptides and proteins are frequently used to determine their secondary structure composition. Thus far, however, this analytical approach is generally a low-resolution technique, particularly because it mostly discriminates only between a-helical, b-sheet (parallel and antiparallel) and so-called random coil conformations. This study shows that for tetrapeptides the combined use of the IR and Raman amide I band profiles allows one to discriminate currently known secondary structure motifs. To exploit the spectral information to its fullest extent, we developed an algorithm which calculates the amide I intensity profiles of IR, isotropic and anisotropic Raman scattering and also the depolarization ratios of the Raman bands as a function of the dihedral angles of the two central amino acid resides. The approach is based on a quantum mechanical treatment of the vibrational coupling between the amide I modes of the three peptide groups in the framework of a coupled oscillator model. We calculated the band profiles of a representative set of secondary structures, i.e. a right-handed a-helix, a 3 10 -helix, b-sheets and a polyproline II (PPII)-type 3 1 -helix and b-turns. Our results unambiguously show that all these secondary structure motifs can be identified by comparing experimentally observed IR and Raman amide I bands with their respective calculated intensity distributions.

Probing conformational propensities of histidine in different protonation states of the unblocked glycyl‐histidyl‐glycine peptide by vibrational and NMR spectroscopy

“…Excitonic coupling of the two modes causes some delocalization, which we utilize for our conformational analysis . The non‐coincidence between IR and isotropic Raman profile with the higher intensity at the lower and higher wavenumber band position, respectively, is diagnostic of a dominant sampling of conformations in the upper left quadrant of the Ramachandran plot, in line with what we earlier observed for most though not all GxG peptide . The VCD signal is heavily negatively biased, which indicates that a comparatively strong negative couplet is superimposed by a rather intense negative signal that can be attributed to an intrinsic magnetic transition dipole moment, which appears in many spectra of cationic GxGs .…”

“…As indicated above, the analysis of the measured amide I′ Raman profiles of GHG in both protonated states were complicated by additional non‐structure related effects. Generally, the depolarization ratios of the two Raman bands of tripeptides have slightly different depolarization ratios, with somewhat higher values for the low wavenumber than for the high wavenumber band (~0.2 vs ~0.14) . These values reflect the dominantly isotropic character of amide I Raman scattering and the fact that the low wavenumber band is assignable to an out‐of‐phase mixture of the two local amide I′ modes .…”

Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy

“…This approach is based on various theoretical frameworks published in preceding years that used excitonic Hamiltonian models to calculate amide-I IR and Raman spectra of peptides and proteins. Linear (steady-state) amide-I IR spectra of proteins were calculated with excitonic coupling models in refs − ; Huang and Schweitzer-Stenner and Tsuboi et al performed such calculations to predict the Raman spectra of proteins, and Gorbunov et al, Falvo et al, Ganim et al, and Hamm et al , created similar excitonic models for interpreting nonlinear amide-I 2D-IR protein spectra.…”

“…Also, the couplings can be estimated at varying levels of complexity. The earliest model developed for the calculation of IR and Raman spectra is the transition dipole coupling (TDC) model, which has been used in many publications since (e.g., refs and − ). In this model, the coupling between transition dipole moments is given by a Coulomb-like model based on the relative orientation and distance between the transition dipole moments (see Figure ).…”

The combined use of amide I bands in polarized Raman, IR, and vibrational dichroism spectra for the structure analysis of peptide fibrils and disordered peptides and proteins

“…This is due to spectroscopic properties of right‐handed helical conformations for which the high wavenumber band becomes predominant in both Raman as well as in the IR spectrum. [ 94 ] Because the corresponding VCD couplet is positive, it neutralizes most of the negative couplet of, for example, pPII. As a consequence, the VCD signal is substantially weaker.…”