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At least 1,369 records · Page 76Linked to original sources
PubMed1975

Conformational and spectral analysis of the polypeptide antibiotic N-methylleucine gramicidin S dihydrochloride by nuclear magnetic resonance.

The 220-MHz proton magnetic resonance spectrum of the cyclic decapeptide antibiotic, mono-N-methylleucine gramicidin S, is reported and all the resonances have been assigned to specific protons of the constituent amino acids. Three methods--temperature dependence and solvent mixture (methanol-trifluoroethanol and dimethyl sulfoxide-trifluoroethanol) dependence of peptide NH proton chemical shifts and proton deuteron exchange--habe been utilized to delineate peptide NH protons. The results of the above methods, coupled with the observed vicinal alpha-CH-NH coupling constants and chemical shifts, indicate that in trifluoroethanol the peptide NH PROTONS OF D-Phe4, D-Phe9, L-Orn2, and L-Val6 are exposed to the sovent, and those of L-Val1, L-Orn7, and L-Leu8 are solvent shielded and intramolecularly hydrogen bonded. In trifluoroethanol, dimethyl sulfoxide, and methanol, the decapeptide has no C2 symmetry, and there are only minor conformational differences in the different solvents. In the proposed conformation in trifluoroethanol, one-half of the decapeptide retained the hydrogen bonding pattern of gramicidin S, i.e. cyclo-(L-Val1 NH--O-C L-Leu8) (a beta turn) and cyclo-(L-Leu8 NH--O-C L-Val1). The second half of the molecule exhibits a different type of stable beta turn involving the ten-atom hydrogen-bonded ring, cyclo-(L-Orn7-NH--O-C D-PHE4).

Computers↗
PubMed2005

XAFS spectral analysis of the cadmium coordination geometry in cadmium thiolate clusters in metallothionein.

We report the combination of measurement and prediction of X-ray absorption fine structure (XAFS) data, where the term XAFS refers to the overall spectrum that encompasses both the X-ray Absorption Near Edge Structure (XANES) region as well as the Extended X-ray Absorption Fine Structure (EXAFS) region, to evaluate the cadmium thiolate cluster structures in the metalloprotein metallothionein. XAFS spectra were simulated using coordinates from molecular models of the protein calculated by molecular mechanics/molecular dynamics (MM3/MD), from NMR analyses, and from analysis of X-ray diffraction data. XAFS spectra were also simulated using the coordinates from X-ray crystallographic data for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, and [Cd4(mu-SPh)6(SPh)4]2-. The simulated XAFS data that were calculated using the FEFF8 program closely resemble the experimental data reported for [Cd(SPh)4]2-, CdS, [Cd2(mu-SPh)2(SPh)4]2-, [Cd4(mu-SPh)6(SPh)4]2-, rabbit liver metallothionein cadmium alpha-domain (Cd4-alpha MT), and cadmium rabbit liver betaalpha metallothionein (Cd7-betaalpha MT). MM3 force field parameters were modified to include cadmium-sulfur bonding and were initially set to values derived from published X-ray diffraction and EXAFS experimental data. The force field was further calibrated and adjusted through comparison between experimental spectra taken from the literature and simulated XAFS spectra calculated using the FEFF8 program in combination with atomic coordinates from MM3/MD energy minimization. MM3/MD techniques were used with the calibrated force field to predict the high-resolution structure of the metal clusters in rabbit liver Cd7-MT. Structures for Cd3S9 (beta) MT and Cd4S11 (alpha) MT domains from MM3/MD calculations and those previously reported for Cd7-MT on the basis of 1H and 113Cd NMR data were compared. Structural differences between the different models for these cadmium thiolate clusters were evident. Combining the measurement and simulation of XAFS data provides an excellent method of assessing, modeling, and predicting metal-binding sites in metalloproteins when X-ray absorption spectroscopy (XAS) data are available.

Animals↗
PubMed1999

Trinuclear Zinc(II) Complexes and Polymeric Cadmium(II) Complexes with the Ligand 2,5-Bis(2-pyridyl)pyrazine: Synthesis, Spectral Analysis, and Single-Crystal and Powder X-ray Analyses.

Three zinc compounds, [ZnCl(2)(bppz)(dmf)] (1), [Zn(3)(OAc)(6)(bppz)(2)](H(2)O) (2), and [Zn(3)(Cl)(6)(bppz)(3)](H(2)O) (3), and two cadmium complexes, {[Cd(OAc)(2)(bppz)](H(2)O)(5)}(n)() (4) and [Cd(NO(3))(2)(bppz)](n)() (5), where bppz is 2,5-bis(2-pyridyl)pyrazine, have been synthesized and characterized spectroscopically and crystallographically. The mononuclear complex 1, C(17)H(17)Cl(2)N(5)OZn, crystallizes in the monoclinic space group P2(1)/c, with a = 8.654(1) Å, b = 9.500(1) Å, c = 22.997(1) Å, beta = 97.99(1) degrees, and Z = 4; R1 for 2356 observed reflections [I > 2sigma(I)] was 0.058. The zinc atom has a distorted square planar coordination sphere with the ligand bppz connected in a mono-bidentate manner. The remaining coordination sites are occupied by the chloride counterions and by an oxygen atom of a solvent molecule. The trinuclear zinc compound 2, C(40)H(38)N(8)O(12)Zn(3).H(2)O, crystallizes in the triclinic space group P&onemacr;, with a = 12.238(4) Å, b = 12.986(3) Å, c = 15.470(4) Å, alpha = 75.65(1) degrees, beta = 97.99(1) degrees, gamma = 65.98(1) degrees, and Z = 2; R1 for 4511 observed reflections [I > 2sigma(I)] was 0.07. This complex consists of a linear arrangement of three zinc atoms. The central zinc atom, located on a crystallographic inversion center, is connected by six bridging acetate groups to two symmetry-related zinc atoms. It has an almost perfect octahedral coordination environment. The outer symmetry-related zinc atoms are in a square pyramidal environment, and they coordinate to three acetate groups and to one bppz molecule in a mono-bidentate manner. Compound 3, C(42)H(30)Cl(6)N(12)Zn(3).1.25H(2)O, a cyclic zinc(II) trimer, crystallizes in the cubic space group Ia&thremacr;d, with a = 26.311(1) Å and Z = 16; R1 for 692 observed reflections [I > 2sigma(I)] was 0.038. This trinuclear complex has a perfect triangular arrangement of the zinc atoms. Each zinc atom is connected to the other two by a bppz molecule. The coordination about the metal is best described as a distorted octahedral with four long distances in the basal plane, to two chlorines and to two nitrogen atoms, and two short distances in the axial direction, to two nitrogen atoms. With Cd(II) two polymeric complexes, 4 and 5 were obtained. Compound 4, C(18)H(16)N(4)O(4)Cd.5H(2)O, crystallizes in the triclinic space group P&onemacr;, a = 9.045(1) Å, b = 10.438(1) Å, c = 12.719(1) Å, alpha = 100.48(1) degrees, beta = 95.05(1) degrees, gamma = 95.86(1) degrees, and Z = 2; R1 for 3694 observed reflections [I > 2sigma(I)] was 0.029. The analogous Cd(NO(3))(2) complex with bppz, 5, could only be obtained in microcrystalline form, and its structure was solved by the use of X-ray powder diffraction methods. Compound 5, C(14)H(10)N(6)O(6)Cd, crystallizes in the monoclinic space group C2/c, with a = 11.6601(3) Å, b = 11.9870(3) Å, c = 12.1453(3) Å, beta = 103.348(2) degrees, and Z = 4. In both 4 and 5 the cadmium atoms are bridged by the ligand bppz, so forming uniform one-dimensional coordination polymers. The cadmium ions exhibit the rare coordination number of 8, with two coordinated ligand molecules and two chelating acetate (4) or nitrate (5) groups.

Journal Article↗
PubMed2005

Thermo-FTIR spectroscopic study of the siderophore ferrioxamine B: spectral analysis and stereochemical implications of iron chelation, pH, and temperature.

FTIR spectra of the microbial siderophore, ferrioxamine B, and its nonchelated form (iron free; desferrioxamine B) were studied to facilitate in-depth investigation on the undisrupted structure of the siderophore and its interactions with the environment. Effects of iron chelation as well as those of various levels of pH and temperature on the stereochemical structure of the free ligand and the ferric complex were examined. The presence of a number of functional groups in these compounds and the mutual interaction between them resulted in significant shifts and overlapping of their characteristic absorption bands. Thermal and pH treatments combined with a comprehensive use of curve-fitting analysis facilitated bands resolution. Absorption bands of all functional groups were identified. The results imply that the compact and rigid structure of the ferric complex (ferrioxamine B) is sustained by intense and specific intramolecular hydrogen bonds. Dehydration was the main process observed at low temperature (25-60 degrees C). At 105 degrees C the free ligand form (desferrioxamine B) had already begun to decompose, whereas ferrioxamine B exhibited stability. The thermal destruction became acute at the 170 degrees C treatment for both molecules. The secondary amide groups and the hydroxamate groups, which comprise the binding site for the Fe atom in the complex, were found to be the most sensitive to the thermal degradation. Significant pH effects were observed only for desferrioxamine B samples at pH 9, accompanied by partial decomposition, similar to that observed at 105 degrees C. Deprotonation of desferrioxamine B was found to begin with the deprotonation of the NH(3+) group. Characteristics of the rigid conformational structure of the ferric complex and the state of the NH(3+) group, both assumed to play an important role in the recognition and uptake of the siderophore by membranal receptors, were elaborated by means of FTIR and are discussed in detail.

Deferoxamine↗
PubMed1999

Raman spectral analysis in the C-H stretching region of proteins and amino acids for investigation of hydrophobic interactions.

Raman spectra of amino acids showed complexity in the C-H stretching region (2800-3100 cm(-)(1)) attributed to diversity of CH, CH(2), and CH(3) groups in the side chains, ionization state, and microenvironment. The involvement of specific amino acids in the C-H stretching region of selected proteins, namely, lysozyme, alpha-lactalbumin, beta-lactoglobulin, and their binary mixtures, was investigated by deconvolution using maximum likelihood techniques. The main protein band near 2940 cm(-)(1) was attributed not only to aromatic and aliphatic amino acids but also to many other amino acids. A band near 3065 cm(-)(1) was assigned to aromatic residues, whereas bands near 2880 and 2900 cm(-)(1) corresponded primarily to aliphatic amino acids. Heating at 90 degrees C increased relative intensity near 2940 cm(-)(1) and decreased relative intensity at 2895-2902 cm(-)(1) for lysozyme and its mixtures with alpha-lactalbumin or beta-lactoglobulin. Additional bands at 2812 or 2838 and 3003 cm(-)(1) were observed after heating or in 8 M deuterated urea, reflecting changes upon denaturation.

Amino Acids↗
PubMed1985

Conformationally restricted C-terminal peptides of substance P. Synthesis, mass spectral analysis and pharmacological properties.

Four cyclic analogues of the C-terminal hepta- or hexapeptide of substance P were prepared by the solution method. The cyclizations were obtained by substituting with cysteine the residues normally present in positions 5 or 6 or 11 of substance P and by subsequent disulfide bond formation. The final products were identified by ordinary analytical procedures and advanced mass spectroscopy. The biological activities were determined on three bioassays: the guinea pig ileum, the guinea pig trachea and the rabbit mesenteric vein. Results obtained with these assays indicate that all peptides with a disulfide bridgehead in position 11 are inactive and that a cycle between positions 5 and 6 already strongly reduces the biological activity. The acyclic precursors containing thiol protection groups display weak biological activities. These results further underline the importance of the side chain in position 11 of substance P and suggest that optimal biological activities may require a linear peptide sequence.

Animals↗
PubMed2006

A new approach to the spectral analysis of liquid membrane oscillators by Gábor transformation.

Liquid membrane oscillators very frequently have an irregular oscillatory behavior. Fourier transformation cannot be used for these nonstationary oscillations to establish their power spectra. This important point seems to be overlooked in the field of chemical oscillators. A new approach is presented here based on Gábor transformation allowing one to obtain power spectra of any kind of oscillations that can be met experimentally. The proposed Gábor analysis is applied to a liquid membrane oscillator containing a cationic surfactant. It was found that the power spectra are strongly influenced by the presence of various added substances.

Journal Article↗
PubMed2006

Detection and spectral analysis of trifluoromethyl groups at a surface by sum frequency generation vibrational spectroscopy.

Sum frequency generation (SFG) vibrational spectroscopy was used to detect the presence of trifluoromethyl groups on the surface of 4-(trifluoromethyl)benzyl alcohol (TFMBA) in air. Supplementary data from infrared and Raman spectra were correlated to ab initio calculations by use of density functional theory (DFT) for TFMBA and three related compounds to reliably assign vibrational modes to the spectra. It was shown that strongly ordered CF3 groups dominate the surface of the TFMBA, and the vibrational modes of this functional group are strongly coupled to the benzene ring of the benzyl alcohol. This coupling, along with the SFG activity of the CF3 group, is removed with the insertion of an oxygen atom between the CF3 group and the benzene ring.

Journal Article↗
PubMedDate not supplied

High-field 1H-NMR spectral analysis of some cucurbitacins.

1H-nmr spectra of the natural products cucurbitacins A, B, C, D, E, F, I, L, 23, 24-dihydrocucurbitacin F, and hexanorcucurbitacin F, as well as three acetylated derivatives, were measured at 360 MHz in pyridine-d5. Chemical shifts and coupling constants were tabulated. In addition to all of the ring and side-chain protons, it was possible to assign several of the hydroxy group signals of these compounds. These compiled data should be useful for the structure determination of new compounds in this series.

Cucurbitacins↗
PubMedDate not supplied

Derivative fluorescence spectral analysis of polycyclic aromatic hydrocarbon-DNA adducts in human placenta.

Metabolic activation in humans of chemical carcinogens found in the environment results in the formation of carcinogen-DNA adducts in vivo. Some polycyclic aromatic hydrocarbon-DNA adducts in human DNA can be hydrolyzed under mildly acidic conditions to yield tetrahydrotetrol derivatives which may then be detected by synchronous fluorescence spectroscopy. In an analysis of human placental DNA, second derivative spectroscopy alone was unable to resolve the synchronous fluorescent signature for r-7,t-8,t-9,c-10-tetrahydroxy-7,8,9,10-tetrahydrobenzo[alpha]pyrene from a crude extract, because a complex array of other fluorescent materials was also present. Purification of the sample by a combination of chromatographic procedures including immunoaffinity chromatography and HPLC has now been shown to yield r-7,t-8,t-9,c-10-tetrahydroxy-7,8,9,10-tetrahydrobenzo[alpha]pyrene residues from human DNA that are spectroscopically pure at the second derivative level. Immunoaffinity columns were prepared with rabbit antiserum raised against DNA that had been modified with (+/-)-r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[alpha]pyre ne. This antiserum has now been shown to recognize DNA samples that have been modified with six different polycyclic aromatic hydrocarbon diol epoxides and is probably only specific for a broad spectrum of polycyclic aromatic hydrocarbon-DNA adducts. Adducts were eluted from the immunoaffinity columns, hydrolyzed with acid, and extracted into isoamyl alcohol, before being subjected to high-performance liquid chromatography. These experiments reveal important limitations of second derivative fluorescence spectroscopy as a tool in the analysis of complex environmental mixtures. Furthermore, they extensively define the ability of anti-benzo[alpha]pyrenediol epoxide-DNA antibodies to recognize different types of polycyclic aromatic hydrocarbon-DNA adducts.

Biotransformation↗