Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

Abstract

Previous perturbation treatments of the Amide I vibrations of 8 polypeptides are inconsistent with a detailed normal coordinate analysis of crystalline polyglycine I. This analysis indicates that the Do interaction constant is essentially zero, rather than the large value (about 20 cm-') required by the earlier application of the perturbation theory. It is suggested that the previously neglected Di, term should be included in the perturbation expression, and it is shown that the physical origin of such a term can be accounted for by transition dipole coupling. This mechanism is shown to give a reasonable explanation of splittings of the C=O stretching vibrations in hydrogenbonded carboxylic acid dimers. Its application to , polypeptides provides a satisfactory interpretation of splittings in the Amide I modes.The useof vibrational spectra to identify different polypeptidechain conformations dates from the work of Elliott and Ambrose (1), who observed that the frequency of the infrared-active Amide I vibration of a polypeptides was about 20 cm-' higher than that of # polypeptides. Further studies on synthetic polypeptides (2) established this observation as a firm empirical rule.Early attempts (3, 4) to account for this difference were not fruitful. A significant advance in understanding the theoretical basis for the above observation was achieved by Miyazawa (5), who developed a perturbation treatment for the interaction of amide-group vibrations in various polypeptide-chain structures. He also noted that, in addition to the strong Amide I band at about 1630 cm-' in the # polypeptides, a weak band at about 1690 cm-' could be assigned to the antiparallel-chain pleated-sheet structure. This treatment has formed the basis for interpretation of the vibrational spectra of polypeptides and proteins (6, 7).In the Miyazawa theory, the frequency of an Amide I mode (which is the only one that we will be concerned with in this paper) is given by p(B,V') = vo + E D,, cos(s8) cos(t') [1] In applications of Eq.[2] to the antiparallel-chain pleatedsheet structure, v(O,Tr) and v(r,O) were taken from the spectrum of polyglycine I, and the frequency of nylon 66 was The above procedure has been criticized (9, 10), primarily on the grounds of the assumed constancy of vo. This criticism was based on studies of a series of polyamides (10) that indicated that jo varied by 6 cm-I between nylon 10 and nylon 2. Such variations can give rise to errors in the interaction constants Do and Do, that are of the same order as the constants themselves. This objection to taking vo from nylon 66 as applicable to polypeptides has a general validity, since it should not be expected that the unperturbed frequency associated with the peptide group is completely independent of the local chemical environment of this group: This is amply established by detailed normal coordinate analyses of N-methyl acetamides and nylons (11), as well as of related molecules (12).It is also confirmed by an extension of these calculations to polyglycines I (13) ...

Understanding the key factors that control the rate of β-hairpin folding

“…1a, the resolution-enhanced (32) FTIR spectrum of trpzip4 at 14.4°C exhibits three resolvable spectral features, centered at Ϸ1,633, 1,655, and 1,676 cm Ϫ1 , respectively. In particular, the pair of lowand high-frequency bands (the 1,633-and 1,676-cm Ϫ1 components, in this case), which originates from vibrational couplings among interstrand amide CAOs, is considered characteristic of antiparallel ␤-sheets (27,28). Consistent with these experimental results, the calculated amide IЈ band of trpzip4, which corresponds to the average of 20 calculated spectra based on the transition dipole coupling model and using the 20 NMR structures of trpzip4 in the Protein Data Bank (ID code 1LE3), also shows three major spectral components (Fig.…”

“…Simulations of the amide IЈ band of the folded and extended structures of tripzip4 were performed with MATLAB (Mathworks, Natick, MA). The method used to generate the amide IЈ band of proteins is based on the transition dipole coupling mechanism (27,28), which attributes the bandwidth and splitting of the amide IЈ manifold to the dipolar interactions or couplings among amide groups. Following Torii and Tasumi (29), we denoted the transition dipole moment of the jth (1 Յ j Յ n) peptide group to ␦ j [in D⅐Å Ϫ1 ⅐atomic mass units (amu) Ϫ1/2 ], the magnitude of which was set to be 3.70 D⅐Å Ϫ1 ⅐amu Ϫ1/2 , and n was the number of peptide bonds.…”

Structure of silk by raman spectromicroscopy: From the spinning glands to the fibers

“…Depending on the dihedral angles of the peptide bonds, the occurrence of hydrogen bonds and the physicochemical environment, the frequency of the skeletal vibrational modes can be shifted, giving insights into protein conformation. The study of silk protein secondary structure can rely on the inestimable pioneering works of Miyazawa et al 18,19 who have performed normal mode analysis of N-methylacetamide, and those of Krimm and coworkers [20][21][22][23][24] who have calculated the normal modes of different synthetic polypeptides such as poly-L-alanine, poly-L-glycine and poly-L-alanylglycine in different conformations.…”

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.…”