Density functional theory DFT(BPW91) level calculations with modified 6-31G(d) basis sets are tested for a small amide, N-methyl acetamide (NMA), as an efficient way for calculating amide I and amide II frequencies that are directly comparable to those commonly measured in solution. The calculational results are compared to experimentally measured FTIR spectra in gas and solution phases. The 6-31G(d) basis set at the DFT level yields vibrational frequencies that have the best agreement with the gas-phase experiment, as compared to amide I and II frequencies calculated with the same basis at the HF, CASSCF, MP2, QCISD, and CCD levels. The DFT(BPW91)/6-31G(d) level calculation for the NMA·3H2O hydrogen-bonded complex with an Onsager or CPCM reaction field yields amide I, II, and III frequencies comparable to the experiment in aqueous solution. The amide I and, to a smaller degree, amide II frequencies are found to be sensitive to the exponent of the d function in the basis set. Use of more diffuse (smaller exponent) d functions in the 6-31G(d) basis set results in a calculated amide I frequency closer to the solution experimental values. Such modified, relatively small basis sets may provide a computationally efficient means of approximating the solvent effects on amide vibrational frequencies.

Ab initio quantum mechanical computations of force fields (FF) and atomic polar and axial tensors (APT and AAT) were carried out for triamide strands Ac-A-A-NH-CH(3) clustered into single-, double-, and triple-strand beta-sheet-like conformations. Models with phi, psi, and omega angles constrained to values appropriate for planar antiparallel and parallel as well as coiled antiparallel (two-stranded) and twisted antiparallel and parallel sheets were computed. The FF, APT, and AAT values were transferred to corresponding larger oligopeptide beta-sheet structures of up to five strands of eight residues each, and their respective IR and vibrational circular dichroism (VCD) spectra were simulated. The antiparallel planar models in a multiple-stranded assembly give a unique IR amide I spectrum with a high-intensity, low-frequency component, but they have very weak negative amide I VCD, both reflecting experimental patterns seen in aggregated structures. Parallel and twisted beta-sheet structures do not develop a highly split amide I, their IR spectra all being similar. A twist in the antiparallel beta-sheet structure leads to a significant increase in VCD intensity, while the parallel structure was not as dramatically affected by the twist. The overall predicted VCD intensity is quite weak but predominantly negative (amide I) for all conformations. This intrinsically weak VCD can explain the high variation seen experimentally in beta-forming peptides and proteins. An even larger variation was predicted in the amide II VCD, which had added complications due to non-hydrogen-bonded residues on the edges of the model sheets.

Infrared (IR) and vibrational circular dichroism (VCD) spectra were measured for a series of isotopically ((13)C on two or more amide Cdouble bond]O) labeled, 25 residue, alpha-helical peptides of the sequence Ac-(AAAAK)(4)AAAAY-NH(2) that were also studied in the previous paper. Theoretical IR and VCD simulations were performed for correspondingly isotopically labeled Ac-A(24)-NHCH(3) constrained to an alpha-helical conformation by use of property tensor transfer from density functional theory (DFT) calculations on Ac-A(10)-NHCH(3). The simulations predicted and experiments confirmed that the vibrational coupling constants between i, i + 1 and i, i + 2 residues differ in sign, thus leading to a reversal of the (13)C VCD pattern and explaining the large shift in the (13)C amide I frequency as reported in the previous paper. The sign of the coupling constant remained consistent for larger label separation (with the exception of i, i + 4) and for more labels with uniform separation. Such effects confirm that the isotopically labeled group vibrations are essentially only coupled to each other and are effectively uncoupled from those of the unlabeled groups. This development confirms the utility of isotopic labels for site-specific structural studies with vibrational spectra. Observed spectral effects cannot be explained by considering only transition dipole coupling (TDC) between amide oscillators, particularly for smaller label separations, but the TDC and ab initio predicted couplings roughly converge at large separation.

Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form ␣-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the ␣-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5°C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis.

SYNOPSISThe "random coil" conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro),] and poly( L-proline). VCD, ir and uv CD spectra of blocked L-proline oligopeptides [(Pro),, n = 2-12] in different solvents are reported and compared to the spectra of poly (L-proline) 11, poly( L-glutamic acid), and unblocked proline oligomers. Based on the chain-length dependence of the VCD and electronic CD (ECD) spectra of proline oligomers, it is established that VCD spectra are dominated by short-range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly(L-proline) I1 and of similar magnitude to that of (Pro), ( n = 3, 4 ) . Based on the spectral evidence, it is concluded that the "random coil" conformation has a large fraction of helical regions, conformationally similar to the left-handed, 31 polyproline I1 helix, as was previously suggested by Krimm and co-workers. This conclusion is further supported by studies of effects of salt ( CaClz, LiBr, LiC104), temperature (5-75OC), and pH on the VCD spectra of L-proline oligomers, poly( L-proline) 11, and poly(L-glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly (L-glutamic acid) are more flexible than are polyproline or even L-proline oligomers.

Articles you may be interested inSingle-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling An empirical correction to amide group vacuum force fields is proposed in order to account for the influence of the aqueous environment on the CvO stretching vibration ͑amide I͒. The dependence of the vibrational absorption spectral intensities on the geometry is studied with density functional theory methods at the BPW91/6-31G** level for N-methyl acetamide interacting with a variety of of water molecule clusters hydrogen bonded to it. These cluster results are then generalized to form an empirical correction for the force field and dipole intensity of the amide I (CvO stretch͒ mode. As an example of its extension, the method is applied to a larger ͑␤-turn model͒ peptide molecule and its IR spectrum is simulated. The method provides realistic bandwidths for the amide I bands if the spectra are generated from the ab initio force field corrected by perturbation from an ensemble of solvent geometries obtained using molecular dynamic simulations.

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Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.