Low-frequency vibrations in α-helices: Helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories

We present an approach to the analysis of low-frequency (0-200 cm^?1) α-helix vibrations in molecular dynamics simulation. The approach employs the P-Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6. pp. 46–60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repealing units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P-Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm^?1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P-Curves and compared. © 1995 John Wiley & Sons, Inc.     

Laser-Raman study of valinomycin-doped and omega-CD3-labeled phosphatidylcholine liposomes

The relative intensities of the CH stretching vibrations are used to study the interaction of lecithin liposomes with valinomycin, a mobile carrier for alkali ions. In the case of dipalmitoyl lecithin liposomes, the lipid phase transition is not significantly affected by valinomycin. However, in dimyristoylphosphatidylcholine liposomes, the phase transition is broadened by the addition of 1 mol% valinomycin even at low K⁺ concentrations. This indicates that the carrier interacts with the hydrophobic core of the bilayer. In addition, these experiments showed that the lipid phase transitions which are reflected by the methylene groups and the terminal methyl groups are nearly equivalent. Therefore a reevaluation of the assignment of the CH stretching bands seemed necessary. Our Raman spectroscopic investigation of ω-deuterated dipalmitoyl lecithin liposomes improves the assignment of CH stretch vibrations to methylene and methyl groups. The deuteration displaces the methyl group vibrations to the 2050–2250 cm^?1 region and produces gross intensity changes of the bands at 2883 and 2936 cm^?1. These changes lead to the conclusion that both bands arise from vibrations which can be attributed simultaneously to the methylene and methyl groups of the fatty acid chains. The displacement of the CH₃ group vibrations from their original positions enhances the intensity ratios (per centimeter), $\text{2883}\text{2847}$ and $\text{2936}\text{2847}$, for the CH₂- groups which are used to monitor the lipid phase transition, and implies that the contributions of the CH₃ groups to the phase transition curves are unimportant. Our finding that the -CD₃ groups reflect no phase transition supports this statement.     

A homeotic mutation influences the wing vibration patterns during mating in males of the silkworm moth Bombyx mori

An abnormality in the wing vibration pattern in males of the E^Nc homeotic mutant of Bombyx mori was investigated. The wild-type (+/+) males show a switching of the rhythmic wing vibrations from a sequential pattern to an intermittent pattern during mating, whereas the E^Nc mutants show a sequential pattern both before and during mating. Wing motions in +/+ males became small during mating, but those in +/E^Nc males did not. Ablation of the head ganglia of +/+ and +/E^Nc males during mating caused no change in the motor patterns of wing vibrations. Ablation or cooling of the posterior abdomen in the +/+ males during mating caused sequential wing vibrations, suggesting that the change in wing vibrations is induced by signals from the posterior abdomen. The pterothoracic ganglion in the +/E^Nc males is separated into two ganglia, in contrast to the complete ganglionic fusion in the +/+ males. The neurons in the pterothoracic ganglion stained from abdominal nerve cords are homologus in +/+ and +/E^Nc males, but many of these in +/E^Nc males are elongated along the anteroposterior axis. These results suggest that the wing vibration pattern is restricted by genetic factors through reconstruction of the thoracic nervous system during metamorphosis.     

Low-frequency Raman scattering study of six nucleosides

Raman spectroscopy was used to study the low-frequency (?200?cm^?1) vibrations in crystalline samples of six naturally occurring nucleosides: deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), uridine (rU), cytidine (rC), and adenosine (rA). Such low-frequency vibrations are important for biological processes in which the conformation of a nucleic acid molecule changes. These experiments also provide a test for the low-frequency vibrational modes of dT, dC, and dA predicted by Shishkin et al.     

Far-infrared absorption of nucleotides and poly(I)·poly(C) RNA

We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ～25 to ～500 cm^?1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm^?1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm^?1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm^?1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.     

Changes in Raman vibrational bands of calf thymus DNA during the B-to-A transition

The B -to-A conformational transition of calf thymus DNA fibers was followed employing Raman spectroscopy. The transition was induced by soaking DNA fibers in water/ethanol mixtures increasing from 60 to 85% ethanol (v/v). Intensity changes of 17 Raman vibrational bands were quantified in the region from 400 to 860 cm^?1. Two bands at 500 and 784 cm^?1 were employed as internal standards. These bands do not appear to change in intensity with ethanol concentration. Large intensity changes relative to these two bands are observed between 70 and 74% ethanol for backbone vibrations at 708, 808, and 835 cm^?1, and base vibrations at 682, 730, and 750 cm^?1. These results indicate that a highly cooperative conformational change takes place between different portions of DNA in the B -to-A transition. Relative intensity changes preceding the onset of the major transition are observed in only two bands; at 835 cm^?1, assigned to a ribose–phosphate vibration, and at 750 cm^?1, assigned to thymine. The implications of these pretransition changes are discussed.     

Subpicosecond dynamics in nucleotides measured by spontaneous Raman spectroscopy

The band widths in Raman spectra are sensitive to dynamics active on a time scale from 0.1 to 10 ps. The band widths of nucleotide vibrations and their dependence on temperature, concentration, and structure are reported. From the experimental band widths and second moments, it is derived that the adenine vibrations at 725, 1336, 1480, and 1575 cm⁻¹, and the uracil vibration at 787 cm⁻¹, are in the fast modulation limit. The correlation times of the perturbations are faster than 0.4 ps. Thermal melting of the helical structure in polynucleotides results in larger band widths, due to an increase in vibrational dephasing and energy relaxation as a consequence of the increased interaction of the base moieties with the solvent molecules. The band width of the 725 cm⁻¹ adenine vibration is dependent on the type and structure of the backbone. It is found to be perturbed by movements of the sugar-phosphate moiety relative to the base. The band width of the 1575 cm⁻¹ adenine vibration is found to be sensitive to the base-pairing interaction. From a comparison of the band widths in polynucleotides with a different base sequence (homopolymer vs alternating purine-pyrimidine sequence), it is concluded that resonant vibrational energy transfer between the base molecules is not important as a relaxation process for the vibrational band widths of nucleotides. Several theoretical models for the interpretation of band widths are discussed. The theory does not take into account the strong hydrogen-bonding nature water and hence fails to describe the observations in nucleotide-water systems. The bands of the carbonyl stretching vibrations are inhomogeneously broadened. The carbonyl groups have a strong dipolar interaction with the polar water molecules and are therefore strongly perturbed by coupling to the heatbath via hydrogen bonds. © 1997 John Wiley & Sons, Inc. Biopoly 41: 751–763, 1997     

The Raman Spectroscopy,XRD, SEM,and AFM Study of Arabinogalactan Sulfates Obtained Using Sulfamic Acid

The structure of sodium salts of arabinogalactan (AG) sulfates obtained by sulfating AG of larch wood with a sulfamic acid–urea mixture in 1,4-dioxane was studied by the methods of Raman spectroscopy, X-ray diffraction (XRD) phase analysis, scanning electron microscopy (SEM), and atomic force microscopy (AFM). The introduction of sulfate groups into the structure of arabinogalactan was confirmed by the appearance in the Raman spectra of new absorption bands related to the deformation vibrations δ (SO₃) at 420 cm^–1 and δ (О=S=O) at 588 cm^–1, stretching vibrations ν (C–O–S) at 822 cm^–1, symmetrical stretching vibrations ν_s (O=S=O) at 1076 cm^–1, and asymmetric stretching vibrations of ν_as (O=S=O) at 1269 cm^–1. According to the XRD data, the amorphization of arabinogalactan structure occurs during the sulfation process. The SEM method revealed a significant difference in the morphology of the sulfated and starting arabinogalactan. The starting AG consists of particles of predominantly globular shape with a size of 10 to 90 μm; arabinogalactan sulfates, of particles of various shapes with sizes of 1–8 μm. According to the AFM, the surface of sulfated arabinogalactan film consists of rather homogeneous spherical particles about 70 nm in size. The root-mean-square value of the surface roughness is 33 nm. The surface of sulfated AG film does not contain impurities.     

Raman spectroscopic analysis of Dutch Belt rabbit erythrocyte ghosts

Dutch Belt rabbit erythrocyte ghosts have been examined by Raman spectroscopy. An unusually high signal-to-noise spectrum was obtained which enabled assessment of vibrations within 300 cm^?1 of the exciting radiation. Assignment of the observed bands to specific vibrations yielded information concerning membrane fluidity, the conformations of the peptide backbones and disulfide bonds of membrane proteins, and the configurations of lipid unsaturated hydrocarbon side chains.     

Far-infrared spectra of poly(-α-amino acids) with basic alkyl group side chains

Far-infrared spectra in the region from 700 to 60 cm^?1 have been measured for the α-helix structures of poly(L -α-amino-n-butyric acid), poly-L -norvaline, poly-L -norleucine, and poly-L -leucine and for the β-form structures of poly(L -α-amino-n-butyric acid), poly-L -valine, poly(DL -amino-n-butyric acid), poly-DL -norvaline, and poly-DL -norleucine. The changes of the spectra on N-deuteration have been measured in the region between 700 and 400 cm^?1. It is concluded that, the α-helix has characteristic bauds near 690, 650, 610, 380, 150, and 100 cm^?1, and that the β-form has characteristic bands near 700, 240, and 120 cm^?1. The main-chain vibrations in the region from 600 to 200 cm^?1 are strongly coupled with the side-chain deformation vibrations.     

Infrared spectroscopic characterization of copper–polyhistidine from 1,800 to 50 cm−1: model systems for copper coordination

Poly(l-histidine) and imidazole in the presence of copper cations have been investigated by means of Fourier transform infrared (IR) spectroscopy in the mid- and far-IR spectral range to establish specific marker bands of the copper-coordination site in metalloproteins as a function of pH as well as the effect of the coordination on the amino acid contributions. Whereas the well-known mid-IR region was specific for the secondary structure of the protein mimics, the far-IR region included contributions from the metal–ligand vibrations. The addition of copper led to secondary structure changes of poly(l-histidine) at neutral and basic pD and to specific shifts of ring vibrations. At pD 9.5 the addition of copper deprotonated the nitrogen atoms of the imidazole ring and the backbone. At neutral pD the copper cations were coordinated by the N3 atom of the imidazole ring. Copper–imidazole vibrations at neutral pD were observed at 154 and 128 cm⁻¹. Signals observed at 313 and 162 cm⁻¹ were assigned to metal–ligand vibrations arising from copper–poly(l-histidine) complexes with a negatively charged imidazole ring.     

Sound and vibration sensitivity of VIIIth nerve fibers in the grassfrog, Rana temporaria

We have studied the sound and vibration sensitivity of 164 amphibian papilla fibers in the VIIIth nerve of the grassfrog, Rana temporaria. The VIIIth nerve was exposed using a dorsal approach. The frogs were placed in a natural sitting posture and stimulated by free-field sound. Furthermore, the animals were stimulated with dorso-ventral vibrations, and the sound-induced vertical vibrations in the setup could be canceled by emitting vibrations in antiphase from the vibration exciter. All low-frequency fibers responded to both sound and vibration with sound thresholds from 23 dB SPL and vibration thresholds from 0.02 cm/s². The sound and vibration sensitivity was compared for each fiber using the offset between the rate-level curves for sound and vibration stimulation as a measure of relative vibration sensitivity. When measured in this way relative vibration sensitivity decreases with frequency from 42 dB at 100 Hz to 25 dB at 400 Hz. Since sound thresholds decrease from 72 dB SPL at 100 Hz to 50 dB SPL at 400 Hz the decrease in relative vibration sensitivity reflects an increase in sound sensitivity with frequency, probably due to enhanced tympanic sensitivity at higher frequencies. In contrast, absolute vibration sensitivity is constant in most of the frequency range studied. Only small effects result from the cancellation of sound-induced vibrations. The reason for this probably is that the maximal induced vibrations in the present setup are 6–10 dB below the fibers' vibration threshold at the threshold for sound. However, these results are only valid for the present physical configuration of the setup and the high vibration-sensitivities of the fibers warrant caution whenever the auditory fibers are stimulated with free-field sound. Thus, the experiments suggest that the low-frequency sound sensitivity is not caused by sound-induced vertical vibrations. Instead, the low-frequency sound sensitivity is either tympanic or mediated through bone conduction or sound-induced pulsations of the lungs.Abbreviations AP amphibian papilla - BF best frequency - PST peristimulus time     

Observation of small conformational changes in the sperm-whale myoglobin by the far-infrared spectra

Small conformational changes in a molecule of sperm-whale myoglobin in its native solid state for different pH values at room temperature as well as during heat denaturation in alkali medium at different stages of unfolding of the globule were observed by using far-infrared spectroscopy in the region from 30 to 600 cm^?1. The changes appeared in the absorption bands near 420 and 470 cm^?1 ascribed to the side-chain vibrations of helical segments of the myoglobin molecule. For the first time the high structural sensitivity of the far-infrared region of the skeletal vibrations has been confirmed experimentally and the applicability of this technique to globular proteins demonstrated.     

Infrared spectra and normal vibration of β-d-glucopyranose

Infrared spectra of β-d-glucopyranose have been measured in the 4000-50 cm^-1 region and normal vibrations of β-d-glucopyranose have been investigated. The normal coordinates are treated by using the Urey-Bradley force-field, and vibrational assignments of the observed bands are made on the basis of the potential-energy distributions. The calculated vibrational-frequencies agree well with the observed frequencies in the region above 250 cm^-1.     

Shape of the conformational energy surface near the global minimum and low-frequency vibrations in the native conformation of globular proteins

Based on the assumption that the conformational energy surface of a protein molecule can be approximated near the global minimum point by a multidimensional parabola, conformational fluctuations in the native state are discussed. In this approximation the conformational fluctuations can be viewed as excitations of coupled harmonic oscillations of dihedral angles. For the purpose of estimating the range of frequencies vibrations, globular proteins are assumed to made of homogeneous continuous elastic material. The number of vibrational modes in such an elastic body, with the wavelength no less than the characteristic length of an amino acid residue, are estimated roughly to be three times the number of amino acid residues in a protein, which is slightly less than the number of variable dihedral angles in a protein. Their frequencies, when converted to the wavenumber of corresponding light, are found to range from 1.8 × 10 cm^?1 to 2.1 × 10²cm^?1 for a protein with the diameter d = 40 Å, when Young's E = 10¹¹ dyne/cm² is assumed. A significant fraction of the coupled vibrations of dihedral angles in real globular proteins are collective ones, i.e., those involving the whole protein molecules. Based on these results, it concluded that the depth of the global minimum s at least 150 Kcal/mol.     

Raman spectra of chemically modified lysozyme. Oxindole derivatives.

The Raman spectra of oxidation products of lysozyme have been investigated. The protein was oxidized by N-bromosuccinimide and dimethyl sulfoxide/HCl. Depending on the experimental conditions one to six tryptophan residues are oxidized to oxindole. The most prominent difference between the spectra of lysozyme and its oxindole derivatives is the strong band at 1017 cm^?1 which displaces the tryptophan peak at 1010 cm^?1. Other tryptophan bands are also weakened corresponding to the number of the tryptophan side chains destroyed. Shifts are observed in the amide I and in the amide III regions sensitive to conformational changes. These shifts indicate conformational differences in the higher oxidized species and in the native enzyme, although the amide III maxima overlap with a strong oxindole band. Similar effects are observed in the range of the C-C stretching vibrations of the peptide backbone. If more than one tryptophan side chain is oxidized changes have also been found in the S-S stretching range. The evaluation of this effect is difficult because of the strong oxindole vibration appearing in this region. In species oxidized by great excess of N-bromosuccinimide the tyrosine vibrations can no longer be detected, indicating the modification of this amino acid too.     

Infrared absorption and raman scattering of sulfate groups of heparin and related glycosaminoglycans in aqueous solution

The i.r. spectra for aqueous solutions of sulfated glycosaminoglycans and model compounds in the transmittance “window” region of the solvent (1400-950 cm^?1) are dominated by the strong and complex absorption centered at ～1230 cm^?1 and associated with the antisymmetric stretching vibrations of the SO groups. Primary and secondary O-sulfate groups absorb at somewhat higher frequencies (1260-1200 cm^?1) than N-sulfates (～1185 cm^?1). Each sulfate band lends itself to quantitative applications, especially within a given class of sulfated polysaccharide. Laser-Raman spectra of heparin and model compounds have been obtained in aqueous solution and in the solid state. The most-prominent Raman peak (at ～1060 cm^?1) is attributable to the symmetrical vibration of the SO groups, with N-sulfates emitting at somewhat lower frequencies (～1040 cm^?1) than O-sulfates. The Raman pattern in the 950-800 cm^?1 region (currently used in the i.r. for distinguishing between types of sulfate groups) also involves vibrations that are not localized only in the COS bonds.     

Raman spectroscopic study of poly (β-benzyl-L-aspartate) and sequential polypeptides

Poly-β-benzyl-L -aspartate (poly[Asp(OBzl)]) forms either a lefthanded α-helix, β-sheet, ω-helix, or random coil under appropriate conditions. In this paper the Raman spectra of the above poly[Asp(OBzl)] conformations are compared. The Raman active amide I line shifts from 1663 cm^?1 to 1679 cm^?1 upon thermal conversion of poly[Asp(OBzl)] from the α-helical to β-sheet conformation while an intense line appearing at 890 cm^?1 in the spectrum of the α-helix decreases in intensity. The 890 cm^?1 line also displays weak intensity when the polymer is dissolved in chloroform–dichloroacetic acid solution and therefore is converted to the random coil. This line probably arises from a skeletal vibration and is expected to be conformationally sensitive. Similar behavior in the intensity of skeletal vibrations is discussed for other polypeptides undergoing conformational transitions. The Raman spectra of two cross-β-sheet copolypeptides, poly(Ala-Gly) and poly(Ser-Gly), are examined. These sequential polypeptides are model compounds for the crystalline regions of Bombyx mori silk fibroin which forms an extensive β-sheet structure. The amide I, III, and skeletal vibrations appeared in the Raman spectra of these polypeptides at the frequencies and intensities associated with β-sheet homopolypeptides. Since the sequential copolypeptides are intermediate in complexity between the homopolypeptides and the proteins, these results indicate that Raman structure–frequency correlations obtained from homopolypeptide studies can now be applied to protein spectra with greater confidence. The perturbation scheme developed by Krimm and Abe for explaining the frequency splitting of the amide I vibrations in β-sheet polyglycine is applied to poly(L -valine), poly-(Ala-Gly), poly(Ser-Gly), and poly[Asp(OBzl)]. The value of the “unperturbed” frequency, V₀, for poly[Asp(OBzl)] was significantly greater than the corresponding values for the other polypeptides. A structural origin for this difference may be displacement of adjacent hydrogen-bonded chains relative to the standard β-sheet conformation.