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.     

Formation of 19-nor-10-keto-25-hydroxyvitamin D3 in cultured mammalian cells

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.     

Low-frequency vibrational spectra of some homopolypeptides in the solid state

Low-frequency Raman and far-infrared spectra of polyglycine, poly-L -alanine, and poly-L -valine have been measured. The Raman spectra exhibit an intense band near 100 cm^?1 for these homopolypeptides. Lattice calculations of the polyglycines are used to assign the intense Raman band to a rotary lattice mode. For homopolypeptides in the β conformation, an infrared band is observed whose frequency varies inversely with the square root of the mass of the peptide repeating unit. This infrared band is assigned to the hydrogen bond stretching lattice vibration.     

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.     

Vibrational analysis of peptides,polypeptides, and proteins. XXIV. Conformation of poly(α-aminoisobutyric acid)

Raman and polarized ir spectra have been obtained on built-up monomolecular films of poly(α-aminoisobutyric acid), and analyzed in the context of normal mode calculations on 3₁₀-, α-, and α′-helix conformations of this molecule. The average discrepancy between observed and calculated frequencies is significantly smaller for the 3₁₀-helix than for the other structures. This, together with the more satisfactory explanation of several special features of the spectra, indicates that this polypeptide adopts a 3₁₀-helix conformation in such thin films.     

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.     

Raman studies of nucleic acids. VII. Poly A-poly U and poly G-poly C

Laser-excited Raman spectra of the double-helical complexes poly A·poly U and poly G·poly C are reported for ²H₂O and H₂O solutions. The spectra are discussed in relation to their use as quantitative reference spectra for determining the dependence of the Raman scattering of RNA on secondary structure. The Raman line at 815 cm^?1, due to the phosphodiester group, exhibits the same intrinsic intensity in spectra of poly A·poly U and poly G·poly C and is thus dependent only upon the amount of ordering of the helix and not on the kinds of nucleotides involved. The hypochromic Raman lines in spectra of poly A·poly U are identified and their intensity changes are determined quantitatively over the temperature range 32–85°C. Comparison of the spectra in the 1500–1750 cm^?1 region reveals that the Raman lines from carbonyl group vibrations of uracil are about sevenfold more intense than those of guanine and cytosine for both paired and unpaired states and will thus dominate the spectra of RNA. The Raman frequencies in this region are also compared with previously reported infrared frequencies and give evidence of being strongly perturbed by base-stacking interactions in the helices.     

A vitrational study of poly (L-proline) I and II in the far infrared.

The far infrared spectra of poly(L -proline) I (190–35 cm^?1) and II (400–35 cm^?1) were obtained in the solid state at both 300° and 110°K. A significant difference in the region below 100 cm^?1 was observed. A very intense band located at 60 cm^?1 in the infrared spectrum of form II has no counterpart in form I. This indicates the sensitivity of low-frequency vibrations to the difference in conformation assumed by both forms in the solid state. Additional bands observed in this study are correlated with ir and Raman data previously reported and tentative assignments are made using the results of normal mode calculations (in the single-chain approximation) which have been reported.     

Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA.

Raman spectra of poly(dG-dC) . poly(dG-dC) in D2O solutions of high (4.0M NaCl) and low-salt (0.1M NaCl) exhibit differences due to different nucleotide conformations and secondary structures of Z and B-DNA. Characteristic carbonyl modes in the 1600-1700 cm-1 region also reflect differences in base pair hydrogen bonding of the respective GC complexes. Comparison with A-DNA confirms the uniqueness of C = O stretching frequencies in each of the three DNA secondary structures. Most useful for qualitative identification of B, Z and A-DNA structures are the intense Raman lines of the phosphodiester backbone in the 750-850 cm-1 region. A conformation-sensitive guanine mode, which yields Raman lines near 682, 668, or 625 cm-1 in B (C2'-endo, anti), A (C3'-endo, anti) or Z (C3'-endo, syn) structures, respectively, is the most useful for quantitative analysis. In D2O, the guanine line of Z-DNA is shifted to 615 cm-1, permitting its detection even in the presence of proteins.     

Probing the photoreaction mechanism of phytochrome through analysis of resonance Raman vibrational spectra of recombinant analogues

Resonance Raman spectra of native and recombinant analogues of oat phytochrome have been obtained and analyzed in conjunction with normal mode calculations. On the basis of frequency shifts observed upon methine bridge deuteration and vinyl and C(15)-methine bridge saturation of the chromophore, intense Raman lines at 805 and 814 cm(-)(1) in P(r) and P(fr), respectively, are assigned as C(15)-hydrogen out-of-plane (HOOP) wags, lines at 665 cm(-)(1) in P(r) and at 672 and 654 cm(-)(1) in P(fr) are assigned as coupled C=C and C-C torsions and in-plane ring twisting modes, and modes at approximately 1300 cm(-)(1) in P(r) are coupled N-H and C-H rocking modes. The empirical assignments and normal mode calculations support proposals that the chromophore structures in P(r) and P(fr) are C(15)-Z,syn and C(15)-E,anti, respectively. The intensities of the C(15)-hydrogen out-of-plane, C=C and C-C torsional, and in-plane ring modes in both P(r) and P(fr) suggest that the initial photochemistry involves simultaneous bond rotations at the C(15)-methine bridge coupled to C(15)-H wagging and D-ring rotation. The strong nonbonded interactions of the C- and D-ring methyl groups in the C(15)-E,anti P(fr) chromophore structure indicated by the intense 814 cm(-1) C(15) HOOP mode suggest that the excited state of P(fr) and its photoproduct states are strongly coupled.     

Infrared and Raman spectra of phosphatidyl-ethanolamine and related compounds.

Infrared and Raman spectra of phosphatidylethanolamine from Escherichia coli, L-alpha-glycero-phosphorylethanolamine and 0-phosphorylethanolamine were obtained. Most of the bands were assigned to each vibrational mode based on the N deuteration effect, comparison of the intensity in the infrared and Raman spectra and the depolarization degree measurement in the Raman spectra. The spectra of phosphatidylethanolamine can be interpreted by assuming that the molecule takes the dipolar ionic structure both in non-polar solvent and in solid.     

Temperature-induced beta-aggregation of fibronectin in aqueous solution

Fibronectin structural reorganization induced by temperature has been investigated by Fourier-transform infrared (FT-IR) spectroscopy and light-scattering experiments.At 20 degrees C, from resolution enhanced by FT-IR spectra, 43% of beta sheet, 31% of turn and 26% of unordered structures were estimated. Static and quasi-elastic light-scattering results do not change significantly between 20 and 34 degrees C. Just below 50 degrees C, a decrease of 1/3 of beta sheet structures contents is observed, concomitantly with a corresponding increase of turn. The contribution of disordered structures is found to be temperature-independent. Above 50 degrees C, our data reveals the formation of intermolecular hydrogen bonding leading to the formation of intermolecular beta sheet structures. The IR band absorption at 1618 cm(-1) increases strongly as a function of temperature. The scattered intensity increases and becomes strongly q(2)-dependent. The dynamic structure factor is not a single exponential decay and becomes strongly dependent on the scattering angle. These results demonstrate that aggregation occurs in fibronectin solution. When temperature decreases, this aggregation is found irreversible.Fibronectin aggregation is driven by the formation of intermolecular hydrogen bonds responsible for intermolecular beta sheet structures.     

Circular dichroism studies of acetylcholinesterase conformation. Comparison of the 11 S and 5.6 S species and the differences induced by inhibitory ligands

Circular dichroism studies were carried out in the vacuum ultraviolet region for 11 S and 5.6 S species of acetylcholinesterase from Torpedo. As the 5.6 S acetylcholinesterase forms larger oligomers in the absence of detergent, the CD spectrum was measured both with and without detergent. Secondary structure analysis of the CD spectrum for 11 S acetylcholinesterase shows 33% alpha-helix, 23% beta-sheet (14% antiparallel and 9% parallel), 17% turns and 26% other structure. Binding of edrophonium to the active site of 11 S acetylcholinesterase increases alpha-helix, while binding of propidium to the peripheral site increases beta-sheet. The beta-sheet content is slightly higher for 5.6 S than 11 S acetylcholinesterase in water. When the detergent is added to 5.6 S acetylcholinesterase, the 190 nm and 220 nm bands become less intense, although the analyses of the two spectra are similar. No significant change is observed for the 5.6 S form in either solvent on binding ligands. The prediction of both parallel and antiparallel beta-sheet suggests that at least one domain in these multidomain proteins belongs to the alpha/beta tertiary structural type.     

Vibrational analysis of peptides, polypeptides, and proteins. XXXII. alpha-Poly(L-glutamic acid)

The Raman and ir spectra of α-helical poly(L -glutamic acid) have been assigned on the basis of a normal mode calculation for this structure. The force field was based on our previously refined main-chain force constants for α-poly(L -alanine) and side-chain force constants for β-calcium–poly(L -glutamate). Despite the identical backbone α-helical structures, significantly different frequencies are calculated, and observed, in the amide III and backbone stretch regions of α-poly(L -glutamic acid), as compared with α-poly(L -alanine). This clearly demonstrates the influence of side-chain structure on mainchain vibrational modes.     

Resonance Raman analysis of the mechanism of energy storage and chromophore distortion in the primary visual photoproduct

The vibrational structure of the chromophore in the primary photoproduct of vision, bathorhodopsin, is examined to determine the cause of the anomalously decoupled and intense C(11)=C(12) hydrogen-out-of-plane (HOOP) wagging modes and their relation to energy storage in the primary photoproduct. Low-temperature (77 K) resonance Raman spectra of Glu181 and Ser186 mutants of bovine rhodopsin reveal only mild mutagenic perturbations of the photoproduct spectrum suggesting that dipolar, electrostatic, or steric interactions with these residues do not cause the HOOP mode frequencies and intensities. Density functional theory calculations are performed to investigate the effect of geometric distortion on the HOOP coupling. The decoupled HOOP modes can be simulated by imposing approximately 40 degrees twists in the same direction about the C(11)=C(12) and C(12)-C(13) bonds. Sequence comparison and examination of the binding site suggests that these distortions are caused by three constraints consisting of an electrostatic anchor between the protonated Schiff base and the Glu113 counterion, as well as steric interactions of the 9- and 13-methyl groups with surrounding residues. This distortion stores light energy that is used to drive the subsequent protein conformational changes that activate rhodopsin.     

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.     

An ab initio and DFT study of structure and vibrational spectra of γ form of Oleic acid: Comparison to experimental data

Oleic acid (cis-9-octadecenoic acid) is the most abundant cis-unsaturated fatty acid in nature; it is distributed in almost all organisms. In this work, we present a detailed vibrational spectroscopy investigation of Oleic acid by using infrared and Raman spectroscopies. These data are supported by quantum mechanical calculations, which allow us to characterize completely the vibrational spectra of this compound. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G(d, p) basis set. After a proper scaling the calculated wavenumbers show a very good agreement with the observed values. A complete vibrational assignment is provided for the observed Raman and infrared spectra of Oleic acid. In this work, we also investigate the deviation of vibrational wavenumbers computed with two quantum chemical methods (HF and B3LYP).     

Vibrational analysis of the all-trans retinal protonated Schiff base.

We have obtained Raman spectra of a series of all-trans retinal protonated Schiff-base isotopic derivatives. 13C-substitutions were made at the 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, and 15 positions while deuteration was performed at position 15. Based on the isotopic shifts, the observed C--C stretching vibrations in the 1,100-1,400 cm-1 fingerprint region are assigned. Normal mode calculations using a modified Urey-Bradley force field have been refined to reproduce the observed frequencies and isotopic shifts. Comparison with fingerprint assignments of all-trans retinal and its unprotonated Schiff base shows that the major effect of Schiff-base formation is a shift of the C14--C15 stretch from 1,111 cm-1 in the aldehyde to approximately 1,163 cm-1 in the Shiff base. This shift is attributed to the increased C14--C15 bond order that results from the reduced electronegativity of the Schiff-base nitrogen compared with the aldehyde oxygen. Protonation of the Schiff base increases pi-electron delocalization, causing a 6 to 16 cm-1 frequency increase of the normal modes involving the C8--C9, C10--C11, C12--C13, and C14--C15 stretches. Comparison of the protonated Schiff base Raman spectrum with that of light-adapted bacteriorhodopsin (BR568) shows that incorporation of the all-trans protonated Schiff base into bacterio-opsin produces an additional approximately 10 cm-1 increase of each C--C stretching frequency as a result of protein-induced pi-electron delocalization. Importantly, the frequency ordering and spacing of the C--C stretches in BR568 is the same as that found in the protonated Schiff base.