Mahmoud Ghomi

Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VIII. Amino Acids with Aromatic Side Chains: L-Phenylalanine, L-Tyrosine, and L-Tryptophan

Four out of the 20 natural α-amino acids (α-AAs) contain aromatic rings in their side chains. In a recent paper (J. Phys. Chem. B 2010, 114, 9072-9083), we have analyzed the structural and vibrational features of l-histidine, one of the potent elements of this series. Here, we report on the three remaining members of this family, i.e., l-phenylalanine, l-tyrosine, and l-tryptophan. Their solution (H(2)O and D(2)O) Raman scattering and Fourier transform infrared absorption attenuated total reflection (FT-IR ATR) spectra were measured at room temperature from the species corresponding to those existing at physiological conditions. Because of the very low water solubility of tyrosine, special attention was paid to avoid any artifact concerning the report of the vibrational spectra corresponding to nondissolved powder of this AA in aqueous solution. Finally, we could obtain for the first time the Raman and FT-IR spectra of tyrosine at very low concentration (2.3 mM) upon long accumulation time. To clarify this point, those vibrational spectra of tyrosine recorded either in the solid phase or in a heterogeneous state, where dissolved and nondissolved species of this AA coexist in aqueous solution, are also provided as Supporting Information . To carry out a discussion on the general geometrical and vibrational behavior of these AAs, we resorted to quantum mechanical calculations at the DFT/B3LYP/6-31++G* level, allowing (i) determination of potential energy surfaces of these AAs in a continuum solvent as a function of the torsion angles χ(1) and χ(2), defining the conformation of each aromatic side chain around C(α)-C(β) and C(β)-C(γ) bonds, respectively; (ii) analysis of geometrical features of the AAs surrounded by clusters of n explicit (n = 5-7) water molecules interacting with the backbone and aromatic rings; and (iii) assignment of the observed vibrational modes by means of the theoretical data provided by the lowest energy conformers of explicitly hydrated amino acids.

Analysis of the structural and vibrational properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations

Abstract Vibrational spectra of the major building blocks of RNA (bases and ribonucleosides) have been recorded in solid phase by means of neutron inelastic scattering (NIS) at low temperature ( T =15 K). The NIS technique has been chosen for its particular use in the analysis of the vibrational modes in which hydrogen atom motions are involved. Moreover, in order to assign as accurately as possible the observed vibrational modes, the effect of the H–D isotopic exchange on the labile hydrogens of sugar and bases has also been studied by recording the NIS spectra of deuterated species. To interpret all the above-mentioned set of experimental data, the harmonic force fields of isolated bases and ribonucleosides have been calculated after full geometry optimisation at the density functional theory level. To test the ability of the theoretical force field to reproduce NIS intensities, first-order spectra of all the above-mentioned molecular compounds have been calculated with the unscaled ab initio force field estimated for isolated molecules. In the spectral region above 900 cm −1 , a satisfactory agreement has been obtained between the calculated and observed NIS spectra of the native molecular species. Below 900 cm −1 , where the vibrational modes arising from the N–H and NH 2 wagging modes are located, some discrepancies have however been found on the comparison between the experimental and theoretical results. This disagreement is mainly related to the intermolecular hydrogen bonding occurring in solid phase in which the labile hydrogens are mainly involved. We have verified this fact by analysing the NIS spectra of the labile hydrogen deuterated species of bases and ribonucleosides which reveal a better agreement with the theoretical spectra in the spectral region below 900 cm −1 .

Interpretation of dna vibrational spectra by normal coordinate analysis

1. In the following article we undertake a brief review of the most prominent DNA vibrational markers as observed experimentally by Raman and i.r. spectroscopies on polynucleotides and explain how a simplified valence force field can account for the evolution of the DNA vibrational spectra. 2. Our discussion made as a review of our previous investigations on the interpretation of DNA vibration modes, is based on some of the most characteristic and structure dependent DNA vibrational markers.

Conformational transitions of nucleic acids studied by IR and Raman spectroscopies

Abstract In this short review we first summarize briefly the comparative results obtained in our laboratory by IR and Raman spectroscopies on the right-handed B and the left-handed Z geometries of polynucleotides. The marker IR bands and Raman lines of these conformations are used to present new results concerning the polymorphism of several oligonucleotidic sequences, studied in crystal, solutions and hydrated films by Raman, IR, microRaman and, for the first time, microIR spectroscopies. Finally we give an example of how vibrational spectroscopy can help in the study of interactions between DNAs and drugs. This experimental work has been performed in parallel with a normal coordinate analysis of the DNA marker peaks and this review includes some of the results concerning these calculations and in particular those recently obtained involved with sugar pucker and phosphate backbone markers.

Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. IV. Amino Acids with Hydrophobic Side Chains: L-Alanine, L-Valine, and L-Isoleucine

In the framework of our investigations on the analysis of vibrational spectra of amino acids (AAs) in hydrated media, Raman scattering and Fourier transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of three alpha-amino acids with hydrophobic hydrocarbon side chains, i.e., alanine, valine, and isoleucine, were measured in H2O and D2O solutions. The present data complete those recently published by our group on glycine and leucine. This series of observed vibrational data gave us the opportunity to analyze the vibrational features of these amino acids in hydrated media by means of the density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing five water molecules interacting with H-donor and H-acceptor sites of amino acids are performed and allowed the observed main Raman and infrared bands to be assigned. Additional calculations on a cluster formed by leucine (L) and five water (W) molecules and the comparison of the obtained data with those recently published by our group on L+12W, allowed us to justify the number of hydration considered in the present report.

The peculiar role of cytosine in nucleoside conformational behaviour: Hydrogen bond donor capacity of nucleic bases

According to theoretical calculations, both 2′-deoxycytidine and cytidine show a different energetical behaviour as compared to the other nucleosides. A C–H···O intramolecular hydrogen bond is suspected to greatly influence the conformational behaviour of the nucleosides. The donor atom is the H6 (H8) atom of the pyrimidic (puric) nucleic base and the acceptor atom is the O5′ atom of the sugar. In the present work, we assess the hydrogen bond donor capacity of the H6/H8 hydrogen atom according to the base, by calculating deprotonation energies and electrostatic potentials. This allows us to state precisely that the peculiar behaviour of deoxycytidine expresses itself in the South conformation, and that cytidine does not behave like deoxycytidine.

HYDROGEN BONDING EFFECTS IN QUANTUM MECHANICAL FORE FIELDS OF PYRIMIDINE BASES : URACIL

Abstract Using dihydrate uracil as a model of H-bonded compound formed by a uracil and two water molecules in the vicinity of HN1C2O and HN3C4O groups, DFT molecular orbital calculations have been performed in order to evaluate the changes in its simulated IR spectrum. To estimate the effect of intermolecular interactions on the vibrational properties of pyrimidine bases we have used the B3LYP functional and polarised 6–31G basis sets. The normal mode analysis enables us to assign the 30 modes of uracil, the 6 modes of the two water molecules along with the 12 additional modes resulting from their mutual interactions.

Interpretation of DNA Vibration Modes: III - The Behaviour of the Sugar Pucker Vibration Modes as a Function of its Pseudorotation Parameters

A systematic study of the sugar pucker characteristic vibration modes as a function of its geometrical conformations, has been performed. The present investigation is based on the Wilson GF method and a non-redundant valence force field. The calculated results allow to assign the modes arising mainly from the sugar motions and present in quasi whole vibrational spectra related to the right or left-handed double-helices (i.e., 1050 cm-1, 960 cm-1 and 890 cm-1). Moreover, the conformation dependent modes as those at 860 cm-1 and around 810 cm-1 (A form) as well as the one located around 830 cm-1 (B form) are interpreted by the present investigation. The possibility of the interaction of the latter modes with the phosphate group motions along the DNA double-helical chains are also discussed.

Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations.

A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.

Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion

Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a folded multi-domain protein with an anisometric shape. RTX motifs thus appear remarkably adapted to the structural and mechanistic constraints of the secretion process. In the low calcium environment of the bacterial cytosol, Apo-RD is an elongated disordered coil appropriately sized for transport through the narrow secretion machinery. The progressive folding of Holo-RD in the extracellular calcium-rich environment as it emerges form the T1SS may then favor its unidirectional export through the secretory channel. This process is relevant for hundreds of bacterial species producing virulent RTX proteins.