Interpretation of the resonance Raman spectra of hemoproteins

The interpretation of the resonance Raman spectra of hemoproteins is given based on the normal coordinate analysis of model compounds (Cu octamethylporphin and Cu octaethylporphin). The correlation between the form of normal vibrations and the sensitivity of vibrational frequencies to the valence and spin state of the Fe atom is discussed.     

Distinguishing cell types or populations based on the computational analysis of their infrared spectra

Infrared (IR) spectroscopy of intact cells results in a fingerprint of their biochemistry in the form of an IR spectrum; this has given rise to the new field of biospectroscopy. This protocol describes sample preparation (a tissue section or cytology specimen), the application of IR spectroscopy tools, and computational analysis. Experimental considerations include optimization of specimen preparation, objective acquisition of a sufficient number of spectra, linking of the derived spectra with tissue architecture or cell type, and computational analysis. The preparation of multiple specimens (up to 50) takes 8 h; the interrogation of a tissue section can take up to 6 h (～100 spectra); and cytology analysis (n = 50, 10 spectra per specimen) takes 14 h. IR spectroscopy generates complex data sets and analyses are best when initially based on a multivariate approach (principal component analysis with or without linear discriminant analysis). This results in the identification of class clustering as well as class-specific chemical entities.     

Temperature dependence of the electronic absorption spectra of polynucleotides and their components]

The temperature dependence of UV-absorption spectra of solutions nucleic bases, nucleosides, nucleotides and metilated bases, uncapable of tautomerization has been studied. The nature of such dependence, its connection with hypochromic effect is discussed. It is shown that for some methods of investigating polynucleotides it is necessary to take into account the temperature changes spectra of monomers.     

Calculation and use of protein-derived conformation-related spectra for the estimate of the secondary structure of proteins from their infrared spectra

This paper probes the calculation of conformation-related basis spectra from infrared spectra (amide I′band) of reference proteins of known conformational composition and, with their aid, the computation of conformations from the amide I′ band of globular proteins using in both approaches a least-squares, curve-fitting computer program for the analysis of the spectra. The following results were obtained. The infrared basis spectra for the α-helix conformation, the β-(antiparallel-chain pleated sheet) conformation and the ρ-conformation were calculated and their physical reality was substantiated. The basis spectra were shown to be similar when the absorption contributions of the side chains of amino acids were either neglected or taken into account (uncorrected or corrected basis spectra). The mutual correlation of the basis spectra, quantified by the roots of the diagonal elements of the inverse matrix, was found to be low enough only for the β-conformation to allow a statistically reliable estimate of the β-conformation content of proteins. The comparison of the percentages of the β-conformation derived from x-ray structural analysis or calculated from infrared spectra showed the suitability of the basis spectra for the rough estimate of the β-conformation percentages of proteins. The results were not significantly different when using the uncorrected or corrected basis spectra.     

A comparative study of the infrared difference spectra for octopus and bovine rhodopsins and their bathorhodopsin photointermediates

Fourier-transform infrared difference spectroscopy has been used to detect the vibrational modes in the chromophore and protein that change in position and intensity between octopus rhodopsin and its photoproducts formed at low temperature (85 K), bathorhodopsin and isorhodopsin. The infrared difference spectra between octopus rhodopsin and octopus bathorhodopsin, octopus bathorhodopsin and octopus isorhodopsin, and octopus isorhodopsin and octopus rhodopsin are compared to analogous difference spectra for the well-studied bovine pigments, in order to understand the similarities in pigment structure and photochemical processes between the vertebrate and invertebrate systems. The structure-sensitive fingerprint region of the infrared spectra for octopus bathorhodopsin shows strong similarities to spectra of both all-trans-retinal and bovine bathorhodopsin, thus confirming chemical extraction data that suggest that octopus bathorhodopsin contains an all-trans-retinal chromophore. In contrast, we find dramatic differences in the hydrogen out-of-plane modes of the two bathorhodopsins, and in the fingerprint lines of the rhodopsins and isorhodopsins for the two pigments. These observations suggest that while the primary effect of light in the octopus rhodopsin system, as in the bovine rhodopsin system, is 11-cis/11-trans isomerization, the protein-chromophore interactions for the two systems are quite different. Finally, striking similarities and differences in infrared lines attributable to changes in amino acid residues in the opsin are found between the two pigment systems. They suggest that no carboxylic acid or tyrosine residues are affected in the initial changes of light-energy transduction in octopus rhodopsin. Comparing the amino acid sequences for octopus and bovine pigments also allows us to suggest that the carboxylic acid residues altered in the bovine transitions are Glu-122 and/or Glu-134.     

Polarized infrared spectra of crystalline glycosaminoglycans

Polarized infrared spectra have been recorded for oriented, crystalline specimens of hyaluronates, chondroitin 4-sulfate and 6-sulfate, dermatan sulfate, and a cartilage proteoglycan, having different known chain conformations as determined by X-ray diffraction. The dichroism data for the vibrational modes of the amide and carboxyl groups have been interpreted with respect to the particular molecular structures.     

Fast calculation of the infrared spectra of large biomolecules

Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics trajectories. The Hessian matrix is calculated from force fields because it is not practical to calculate the Hessian from quantum mechanics for large molecules. As an alternative to molecular dynamics the spectral response can be calculated from a time autocorrelation derived from numerical solution of the harmonic equations of motion, resulting in calculations at least 4 times faster. Because the calculation also scales linearly with number of atoms, N, it is faster than normal-mode calculations that scale as N ³ for proteins with more then 4,700 atoms. Using this method it is practical to perform all-atom calculations for large biological systems, for example viral capsids, with the order of 10⁵ atoms.     

A factorization method for the classification of infrared spectra

Background  

Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A convenient application is metabolic monitoring of patients using infrared spectroscopy. Within an infrared spectrum each single compound contributes quantitatively to the measurement.     

Study of the infrared spectra of oligosaccharides in the region 1,000-40 cm-1.

The i.r. spectra of disaccharides differing in monosaccharide composition and in the position and configuration of the glycosidic linkage, and also those of raffinose and model saccharides, were studied in the region 1,000-40 cm-1. Two ranges may be of interest for structural analysis. The first, called "the anomeric region=, is suitable for the determination of the configuration of the glycosidic linkage. The spectra of the oligosaccharides in the second region, called "the region of crystallinity", depend upon the packing of the molecules in the solid. The reasons for the present impossibility of using the far-infrared region of the i.r. spectra of lower oligosaccharides for the determination of the position of the glycosidic linkage are considered.