Infrared amide I' band of the coiled coil.

The Fourier transform infrared (FTIR) spectra of several coiled-coil proteins have been shown to possess unusual features in the amide I' region. Band maxima occur in the vicinity of 1630 cm-1, with component bands at higher frequency. This is well below the observed band at 1650 cm-1 found in standard alpha-helical polypeptides such as poly-L-alanine. Normal mode calculations on models of the coiled-coil structure have been performed to investigate this issue. We find that the observed band profile can be reproduced with very small random variation on the phi, psi of tropomyosin. We believe that the shift to lower frequency is due to additional hydrogen bonding of the solvent accessible backbone CO groups to water.

Vibrational analysis of glutathione.

Infrared and Raman spectra have been obtained of crystalline glutathione and its deuterated derivative and interpreted by normal mode analysis. The force field consisted of our empirical force fields for the peptide group and NH3+ and CO2- end groups, plus our ab initio force fields for the CH2SH and CH2COOH moieties. Observed bands are reproduced with an average error of 5 cm-1, demonstrating that the vibrational spectrum of such a complex molecule can be understood in great depth.

Understanding normal modes of proteins

In order to obtain accurate normal modes of proteins, which is a prerequisite for detailed analyses in a variety of vibrational spectroscopic techniques, reliable conformation-dependent force fields are required. We discuss the use of empirical polypeptide force fields for this purpose, since they have generally been quite successful in reproducing spectra of synthetic polypeptides. Although their limitations are motivating our development of a spectroscopically determined force field (SDFF), empirical force fields can still provide important insights into the normal modes of proteins. We illustrate this by calculations on deoxymyoglobin. Together with ab initio dipole derivatives, amide I and amide II IR band profiles have been computed. These, together with the eigenvectors, show how helix irregularity and force constant variation can influence the delocalization of displacements in the mode, and the shape and breadth of observed bands. The influence of rigid peptide group geometry on the low-frequency density-of-states is also examined.

Vibrational studies of the disulfide group in proteins. VI. General correlations of SS and CS stretch frequencies with disulfide bridge geometry.

Normal mode calculations have been done on a range of disulfide bridge conformations in order to determine how the SS stretch and CS stretch frequencies depend on structure. In addition to varying the C alpha C beta SS and NC alpha C beta S dihedral angles, we have varied the phi, psi of the adjoining peptide groups since we have shown that these also influence the above frequencies. In order to obtain structural information from the observed frequencies, we have done a study of the conformational states found in 92 disulfide bridges in 25 known protein structures. This permits making a statistically based correlation between CS stretch frequencies and the possible contributing conformers.

Vibrational studies of the disulfide group in proteins. Part V. Correlation of SS stretch frequencies with the CCSS dihedral angle in known protein disulfide bridges.

Normal mode calculations have been done on 92 disulfide bridges in 25 known protein structures in order to correlate the SS stretch frequency with the CCSS dihedral angle. It is possible to classify the frequencies into four major categories, which provide a more detailed classification scheme than previously proposed from dialkyl disulfide correlations.

Vibrational analysis of crystalline tri-L-alanine.

We have found that tri-L-alanine (Ala3) can crystallize in a parallel-chain beta structure in addition to the previously known antiparallel-chain beta structure. Although the chain conformations in each structure are essentially similar, the ir and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these differences. This demonstrates the essential validity of our empirically refined force fields, as well as showing that deeper insights into polypeptide and protein structure can be achieved through the rigorous analyses of normal mode calculations.

Vibrational analysis of the structure of gramicidin A. I. Normal mode analysis.

Normal mode frequencies have been calculated for single-stranded beta 4.4 and beta 6.3 and for double-stranded increases decreases beta 5.6, increases decreases beta 7.2, increases increases beta 5.6, and increases increases beta 7.2 helices that are possible models for the structure of gramicidin A. The force field used in the calculations is one that reproduces the frequencies of model polypeptide chain structures to about +/- 5 cm-1, and is therefore expected to provide meaningful distinctions between these conformations. The calculations predict significant differences in the infrared and Raman spectra of these beta-helices, suggesting that they should be identifiable from their spectra (which is shown in the following paper to be the case). The most sensitive region is that of the amide I frequencies, where the predicted patterns of intense infrared mode, infrared splittings, and intense Raman mode provide a characteristic identification of each of the above structures.

Vibrational analysis of the structure of gramicidin A. II. Vibrational spectra.

Raman and infrared spectra have been obtained of gramicidin A (GA) in the crystalline state both in the native form and complexed with CsSCN and KSCN, in solution in dioxane, and incorporated into lipid vesicles. Based on predictions from normal mode calculations of a number of relevant single- and double-stranded beta-helix conformations (Naik and Krimm, 1986), it has been possible to assign the structures of GA that are present under the above conditions. In the crystalline state, native GA has a double-stranded increases decreases beta 5.6 structure, whereas complexes with CsSCN or KSCN adopt a increases decreases beta 7.2 structure. In dioxane solution, the increases decreases beta 5.6 structure predominates. In lipid vesicles, the single-stranded beta 6.3-helix is found, which converts to a double-stranded helix on drying the sample. These results support our previous studies in showing that normal mode analysis can be a powerful technique in obtaining three-dimensional structural information from vibrational spectra.

Vibrational analysis of peptides, polypeptides, and proteins. XXX. Normal mode analyses of gamma-turns.

The normal modes have been calculated for three kinds of low energy gamma-turn structures resulting from recent conformational energy calculations by Némethy. Frequencies have been computed for a gamma-turn, a mirror-related gamma-turn, and an inverse gamma-turn of CH3-CO-(L-Ala)n-NH-CH3, with n = 3 and n = 5, and for certain 14C and 15N derivatives of the n = 3 molecule. Correlations are evident between amide frequencies and gamma-turn structures, and it is found that only amide I modes of peptide groups in the turn are relatively insensitive to the lengths of attached chains.

Vibrational analysis of peptides, polypeptides and proteins. XXVII. Structure of gramicidin S from normal mode analyses of low-energy conformations.

Normal mode calculations have been carried out on three low-energy structures of gramicidin S obtained from conformational energy calculations. When the results on the amide modes are compared with observed bands in the infrared and Raman spectra of crystalline gramicidin S and its N-deuterated derivative, one of the structures is clearly disfavored. Of the other two, one is slightly favored, and it corresponds to the lowest-energy structure obtained from the energy calculations. Spectra from solutions in DMSO and CH3 OH suggest that the molecular conformation is essentially retained in these solvents.

The structure of crystalline and membrane-bound gramicidin A by vibrational analysis.

The results of normal mode calculations on the beta 4.4, beta 6.3, beta 5.6, and beta 7.2 structures of gramicidin A are compared with infrared and Raman spectra of crystalline native, crystalline Cs+-bound, and vesicle-bound gramicidin A. The observed frequencies and frequency splittings are in good agreement with an assignment of beta 5.6, beta 7.2, and beta 6.3 structures, respectively, to the gramicidin A molecules in the above three systems.

Vibrational analysis of peptides, polypeptides, and proteins. XVII. Normal modes of crystalline Pro-Leu-Gly-NH2, a type II beta-turn.

A normal mode calculation has been done for Pro-Leu-Gly-NH2 in its crystalline type II beta-turn structure, and assignments have been made to infrared and Raman bands of this molecule and its N-deuterated derivative. Observed and calculated frequencies below 1700 cm-1 agree to within about 6 cm-1. This analysis provides a sound basis for studying the conformation dependence of the vibrational spectrum.

Infrared spectrum of the purple membrane: clue to a proton conduction mechanism?

The infrared spectrum of the purple membrane of Halobacterium halobium has amide I and amide A frequencies that are anomalously high for standard alpha-helical structures. Normal mode calculations indicate that these and other unusual features of the spectrum can be attributed to alpha 11-helices. Such structures suggest that the helix backbone may provide the framework through which proton transport takes place.