Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

Abstract

Isotopic substitution with 13 C on the amide CdO has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, -forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these -sheet systems the effect of the relative positions of the 13 C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local -structure formation, because coupling between close-lying CdO groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the CdO groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/ 6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results. IntroductionVibrational spectra, IR and Raman, have long been used to determine average secondary structure characteristics in peptides and proteins. 1-4 Like electronic circular dichroic (ECD) structural studies, the limited resolution of vibrational spectra normally provides sequence-averaged structural information in comparison to the localized details derivable from NMR and X-ray diffraction. Since optical spectra can provide inherently fast measures of structure and are generally applicable to all protein and peptide systems, increasing their information content is of wide interest. Vibrational spectra, in contrast to electronic spectra, have distinctive frequency shifts due to isotopic variation, which can be used to give site-specific characteristics to certain bands for selectively labeled peptides. In the past decade a number of studies have appeared where isotopic substitution was used to obtain better structural insight with IR spectra. [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] Isotopic labeling of the amide group has an important impact on vibrational spectra, be...

Cross-Strand Coupling and Site-Specific Unfolding Thermodynamics of a Trpzip β-Hairpin Peptide Using 13C Isotopic Labeling and IR Spectroscopy

“…As in our previous reports for -hairpin isotopic labeling, 52,54,74 the A3K8 and A3A10 labeling patterns develop two distinct 13 CdO amide I band characteristics. On the basis of our calculational models and the similarity with labeled amide I results for previously studied hairpins, we assign the differences to a sign change in the site-specific vibrational coupling interactions.…”

“…As we previously demonstrated, 40,41,52,54,74 the labeling patterns used for A3K8 and A3A10, forming larger (14-atom) and smaller (10-atom) cross-strand 13 C-labeled H-bonded rings (see Scheme 1) develop two distinct 13 CdO vibrational coupling patterns. In A3K8 (large 14-atom ring), the 13 C peak appears at a higher frequency and with greater intensity than in A3A10 (small 10-atom ring).…”

“…The BPW91 functional is faster than the conventionally used hybrid functional (B3LYP) and for the amide I and II bands gives better results, as we have previously shown. 40,54 The resulting FF and APT tensors were transferred toourprogramsforspectralsimulationandisotopicsubstitution. [55][56][57] Comparison of these results provides a simulation of the spectra for models of the folded structure and some evaluation of the effects of distortion of the ideal hairpin geometry.…”

l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra

“…The biggest shift of 57 cm -1 (∼3.4%) is exhibited by the amide I mode (CdO stretching), which is less than the 4.1% [) (13/12) 1/2 -1) × 100%] that might be expected from the carbon mass change, but still slightly more than a 2.3% change similarly estimated from the reduced mass of the CO group. 41 The amide I 13 C-induced shift is conveniently used to monitor mode coupling and conformation of peptides in IR and vibrational circular dichroism studies. 42,43 In our case, the CdO stretching wavenumber shift is not particularly helpful, because the molecule contains only one amide group and the amide I band is well-separated from the other modes.…”

“…The BPW91 functional in smaller basis sets gives a better amide I (∼1650 cm -1 ) frequency than B3LYP (∼1690 cm -1 ), which is very convenient for IR amide I peptide studies. 41,50,51 But this convenience vanishes in the Raman spectroscopy, where the structural information is encoded in many other vibrational transitions. The B3LYP frequencies appear better on average; typically, the BPW91 peak positions are predicted to be too low, including the strongest ROA and Raman bands.…”