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Results for “Spectroscopy, Fourier Transform Infrared”

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PubMed1991

Structural characterization of human lens membrane lipid by infrared spectroscopy.

Fourier transform infrared spectroscopy was used to measure the structural changes in lipid hydrocarbon chain and interface regions of membranes that were obtained from the cortex and the nucleus of the normal human lens. Temperature-dependent studies, ie, phase transitions, were performed to evaluate the differences in the thermodynamic properties of the nuclear and cortical lipids. The structure of the fatty acyl chain region showed a higher degree of order for the nuclear lipid membranes as compared with the cortical ones. At physiologic temperature, the acyl chains of lipid from the cortical region of a 51-yr-old lens showed a degree of disorder of 63 +/- 0.6% compared with 23 +/- 1% for the nuclear region. The gel-to-liquid crystalline-phase transition temperatures were 27.2 +/- 0.3 and 39.2 +/- 1 degree C for the cortical and nuclear lipids, respectively. From the phase transition data, the enthalpy (strength of lipid-lipid interactions), entropy (randomness of the bilayer), and cooperativity (influence of adjacent lipid molecules) were calculated to be 2.6, 1.8, and 2 times greater, respectively, for the nuclear lipid transition compared with the cortical lipid transition. These differences show stronger lipid interactions and higher order in the nuclear membranes as compared with those in the cortex. Energetic differences between the cortical and nuclear membranes may arise from differences in the level of hydration or in the packing at the interface region. This last possibility is supported by changes in the contour of the carbonyl band near 1743 cm-1.

Fourier Analysis↗

PubMedDate not supplied

Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy.

An overview of the application of Fourier transform infrared spectroscopy for the analysis of the structure of proteins and protein-ligand recognition is given. The principle of the technique and of the spectra analysis is demonstrated. Spectral signal assignments to vibrational modes of the peptide chromophore, amino acid side chains, cofactors and metal ligands are summarized. Several examples for protein-ligand recognition are discussed. A particular focus is heme proteins and, as an example, studies of cytochrome P450 are reviewed. Fourier transform infrared spectroscopy in combination with the various techniques such as time-resolved and low-temperature methods, site-directed mutagenesis and isotope labeling is a helpful approach to studying protein-ligand recognition.

Cytochrome P-450 Enzyme System↗

PubMed2002

Identification of scrapie infection from blood serum by Fourier transform infrared spectroscopy.

We describe a new Fourier transform infrared (FT-IR) spectroscopy-based diagnostic approach, which may provide for the first time a rapid, reliable, and inexpensive blood test for scrapie and related transmissible spongiform encephalopathies (TSE). Blood serum from 146 terminally ill Syrian hamsters infected with 263K scrapie via different routes of inoculation and from 166 healthy control animals was analyzed by FT-IR spectroscopy and artificial neural networks (ANN). This revealed characteristic molecular alterations in the serum of infected donors. Different ANN models were constructed and challenged with previously unknown samples in test runs in order to establish whether the new method is able to discriminate between normal and infected animals. Optimized ANNs consistently yielded test sensitivities and specificities of 97% and 100%, respectively. The predictive value of a positive (negative) test was 100% (98%). The proposed serum test circumvents substantial drawbacks of conventional TSE diagnostics and can be fully automated.

Animals↗

PubMed2000

Enhanced prediction accuracy of protein secondary structure using hydrogen exchange Fourier transform infrared spectroscopy.

A novel equilibrium hydrogen exchange Fourier transform IR (HX-FTIR) spectroscopy method for predicting secondary structure content was employed using spectra obtained for a training set of 23 globular proteins. The IR bandshape and frequency changes resulting from controlled levels of H-D exchange were observed to be protein-dependent. Their analysis revealed these variations to be partly correlated to secondary structure. For each protein, a set of 6 spectra was measured with a systematic variation of the solvent H-D ratio and was subjected to factor analysis. The most significant component spectra for each protein, representing independent aspects of the spectral response to deuteration, were each subjected to a second factor analysis over the entire training set. Restricted multiple regression (RMR) analysis using the loadings of the principal components from 19 of these H-D analyses revealed an improvement in prediction accuracy compared with conventional bandshape-based analyses of FTIR data. Nearly a factor of 2 reduction in error for prediction of helix fractions was found using s1, the average spectral response for the H-D set. In some cases, significant error reduction for prediction of minor components was found using higher factors. Using the same analytical methods, prediction errors with this new deuteration-response-FTIR method were shown to be even better than those obtained by use of electronic circular dichroism (ECD) data for helix predictions and to be significantly lower for ECD-based sheet prediction, making these the best secondary structure predictions obtained with the RMR method. Tests of a limited variable selection scheme showed further improvements, consistent with previous results of this approach using ECD data.

Deuterium Oxide↗

PubMedDate not supplied

Rapid method for determining malondialdehyde as secondary oxidation product in palm olein system by Fourier transform infrared spectroscopy.

A simple and rapid Fourier transform infrared (FTIR) spectroscopic method has been developed for the quantitative determination of malondialdehyde as secondary oxidation product in a palm olein system. The FTIR method was based on a sodium chloride transmission cell and utilised a partial least square statistical approach to derive a calibration model. The frequency region combinations that gave good calibration were 2900-2800, and 1800-1600 cm-1. The precision and accuracy, in the range 0-60 mumol malondialdehyde/kg oil, were comparable to those of the modified distillation method with a coefficient of determination (r2) of 0.9891 and standard error of calibration of 1.49. The calibration was cross-validated and produced an r2 of 0.9786 and standard error of prediction of 2.136. The results showed that the FTIR method is versatile, efficient and accurate, and suitable for routine quality control analysis with the result obtainable in about 2 min from a sample of less than 2 mL.

Malondialdehyde↗

PubMed1996

Thiocyanate levels in human saliva: quantitation by Fourier transform infrared spectroscopy.

A new quantitative method, based on Fourier transform infrared spectroscopy, was developed to evaluate the thiocyanate concentration in human saliva. Saliva samples were collected following a typical protocol and infrared spectra obtained from very small volumes (5 microl) deposited on a barium fluoride substrate. Exogenous potassium thiocyanate was used for calibration of the endogenous thiocyanate. This methodology does not require separation or extraction procedures. Human saliva spectra contain a characteristic marker band, due to thiocyanate, at 2058 cm-1. The integrated area of this band can be used for linear regression analysis and provides a good correlation between band area and thiocyanate concentration. Recovery of thiocyanate added to saliva was 100%. Centrifugation and dialysis experiments demonstrated that thiocyanate in saliva exists as a free or loosely bound ion. Saliva collected in the afternoon from 25 different subjects had a thiocyanate concentration of 0.83 +/- 0.42 (mean +/- SD) mmol/liter. In 4 subjects whose circadian pattern was investigated there was evidence of a higher thiocyanate concentration in saliva samples collected in the morning hours.

Cyanates↗

PubMed1997

Structural coupling between the oxygen-evolving Mn cluster and a tyrosine residue in photosystem II as revealed by Fourier transform infrared spectroscopy.

The flash-induced Fourier transform infrared (FTIR) difference spectrum of the oxygen-evolving Mn cluster upon S1-to-S2 transition (S2/S1 spectrum) was measured using photosystem II (PS II) core complexes of Synechocystis 6803 in which tyrosine residues were specifically labeled with 13C at the ring-4 position. The double-difference spectrum between the unlabeled and labeled S2/S1 spectra showed that the bands at 1254 and 1521 cm-1 downshifted by 25 and 15 cm-1, respectively, upon ring-4-13C-Tyr labeling. This observation indicates that there is a tyrosine residue coupled to the Mn cluster, and the vibrational modes of this tyrosine are affected upon S2 formation. From a comparison of the above band positions and isotopic shifts in the S2/S1 spectrum with those of the FTIR spectra of tyrosine in aqueous solution at pH 0.6 (Tyr-OH) and pH 13.4 (Tyr-O-) and of the YD./YD FTIR difference spectrum, the 1254 and 1521 cm-1 bands were assigned to the CO stretching and ring CC stretching modes of tyrosine, respectively, and this tyrosine was suggested to be protonated in PS II. The observation that the effect of the S2 formation on the tyrosine bands appeared as a decrease in intensity with little frequency change could not be explained by a simple electrostatic effect by Mn oxidation, suggesting that the Mn cluster and a tyrosine are linked via chemical and/or hydrogen bonds and the structural changes of the Mn cluster are transmitted to the tyrosine through these bonds. On the basis of previous EPR studies that showed close proximity of YZ to the Mn cluster, YZ was proposed as the most probable candidate for the above tyrosine. This is the first demonstration of the structural coupling between YZ and the Mn cluster in an intact oxygen-evolving complex. This structural coupling may facilitate electron transfer from the Mn cluster to YZ. Our observation also provides an experimental support in favor of the proton or hydrogen atom abstraction model for the YZ function.

Bacterial Proteins↗

PubMed1983

Investigation of the primary photochemistry of bacteriorhodopsin by low-temperature Fourier-transform infrared spectroscopy.

The method of Fourier-transform infrared difference spectroscopy was applied to investigate the transition at 77K of bacteriorhodopsin in its light-adapted form to K6(10), the first intermediate which is stable at low temperature. In addition to unmodified bacteriorhodopsin, bacteriorhodopsin in 2H2O and bacteriorhodopsin containing [15-2H]retinal was used. The results show that major rearrangements occur in the Schiff base in this transition. It is not possible to identify a C = N stretching vibration of the Schiff base in K6(10). The identification of an N-H bending vibration in K6(10) shows that the nitrogen of the previous Schiff base still has a proton attached. The fingerprint region exhibits very unusual features for K6(10) and bears no similarity to protonated retinylidene Schiff base model compounds of any isomeric composition. Therefore, no conclusions on the isomeric state of the retinal in K6(10) can be drawn. The spectra show that the terminal part of the retinal is predominantly reflected in the difference spectra. This indicates that the most polar part of the retinal is located near the Schiff base. We have evidence for protein molecular changes occurring in this transition at 77K.

Bacteriorhodopsins↗

PubMed2005

A matrix isolation study of the photochemically induced reactions of nitrogen dioxide with 1,2-dibromoethene and 1,2-dichloroethene using Fourier transform infrared spectroscopy.

Photolyses of matrices of either BrCHCHBr/NO2/Ar or ClCHCHCl/NO2/Ar using quartz-filtered radiation (lambda>240 nm) led to the appearance of infrared bands attributable to carbonyl, carbon monoxide, and ketene species; no bands belonging to a precursor complex NO2cdots, three dots, centeredXCHCHX (where X=Br or Cl) were observed upon matrix deposition. The possible reaction pathway is discussed.

Bromine↗

PubMed2006

The methyl C-H blueshift in N,N-dimethylformamide-water mixtures probed by two-dimensional Fourier-transform infrared spectroscopy.

Two-dimensional correlation spectroscopy was used to study the composition-dependent spectral variations of the CH-stretching bands of N,N-dimethylformamide (DMF)-water mixtures with X(DMF) ranging from 0.98 to 0.60. By a detailed correlation analysis of the spectral changes of the CH- and OH-stretching bands, it is found that the intensities of the CH and OH bands change in different ways when the water content is increased. It is also found that two different regions of the water content can be distinguished, in which the intensity changes have different signatures. A tentative explanation for how these phenomena might be related to structural changes in the mixture is proposed. The structural change of DMF induced by the water hydrogen bonded on the carbonyl group is supposed to be the possible origin of the methyl C-H blueshift instead of the direct C-H...O interactions before the hydrophobic hydration takes place.

Algorithms↗

PubMed2001

Structural changes in bacteriorhodopsin during the photocycle measured by time-resolved polarized Fourier transform infrared spectroscopy.

The structural changes in bacteriorhodopsin during the photocycle are investigated. Time resolved polarized infrared spectroscopy in combination with photoselection is used to determine the orientation and motion of certain structural units of the molecule: Asp-85, Asp-96, Asp-115, the Schiff base, and several amide I vibrations. The results are compared with recently published x-ray diffraction data with atomic resolution about conformational motions during the photocycle. The orientation of the measured vibrations are also calculated from the structure data, and based on the comparison of the values from the two techniques new information is obtained: several amide I bands in the infrared spectrum are assigned, and we can also identify the position of the proton in the protonated Asp residues.

Aspartic Acid↗

PubMed1997

Characterization of the interaction of Ca2+ with hydroxy and non-hydroxy fatty acid species of cerebroside sulfate by Fourier transform infrared spectroscopy and molecular modeling.

Ca2+-mediated interactions between the carbohydrate groups of glycolipids, including that of cerebroside sulfate (galactosylceramide I3-sulfate), have recently been implicated as a basis of cell recognition and adhesion. Hydroxylation of the fatty acid of this lipid has an effect on these interactions. Therefore, FT-IR spectroscopy was used to study the interaction of Ca2+ with semisynthetic hydroxy (HFA) and non-hydroxy fatty acid (NFA) species of cerebroside sulfate (CBS). Ca2+ caused partial dehydration of the sulfate group and reduced hydrogen bonding of the sugar hydroxyls of both species. The amide I and II bands of the lipids in the absence of Ca2+ (NH4+ salt forms) suggested that the N-H of the HFA species is involved in a bent intramolecular hydrogen bond, probably with the fatty acid hydroxyl group and the glycosidic oxygen, while that of the NFA species is involved in a linear intermolecular hydrogen bond with the C=O and/or other oxygens. Ca2+ caused a rearrangement of the hydrogen-bonding network in the interfacial region of the HFA species involving the amide group. The results suggested increased hydrogen bonding of the C=O and a shift in hydrogen bonding of the N-H of the Ca2+ salt form of the HFA species from a bent intramolecular hydrogen bond to a linear intermolecular hydrogen bond, probably with the C=O of neighboring molecules, similar to the NFA species. The involvement of the fatty acid alpha-hydroxyl group in the rearranged network was indicated by a reduction in mobility of the alpha-CH group of the HFA species, in contrast to that of the NFA species. Participation of the alpha-OH group in hydrogen-bonding networks in the interfacial region of both the NH4+ and Ca2+ salt forms caused a significant increase in the interchain packing, as evident from correlation field splitting of the HFA-CBS methylene scissoring mode, while this did not occur for the NFA species. The absence of intramolecular hydrogen bonding of the N-H with the glycosidic oxygen for both salt forms of the NFA species and for the Ca2+ salt form of the HFA species may destabilize the "bent shovel", bilayer planar conformation of the sugar and cause it to be in the extended, bilayer perpendicular conformation. Calculations of the three-dimensional interaction energy of Ca2+ with CBS showed strong binding around the sulfate and the surface of galactose facing the bilayer in the bent shovel conformation. Ca2+ binding at this surface would disrupt intra- and intermolecular hydrogen-bonding interactions of the head group, thus accounting for its effect in inducing a transition to the extended conformation.

Binding Sites↗

PubMed1988

A study of the structure of human complement component factor H by Fourier transform infrared spectroscopy and secondary structure averaging methods.

Fourier transform infrared spectroscopy was used to investigate the secondary structure of human complement component factor H in H2O and 2H2O buffers. The spectra show a broad amide I band which after second-derivative calculations is shown to be composed of three components at 1645, 1663, and 1685 cm-1 in H2O and at 1638, 1661, and 1680 cm-1 in 2H2O. The frequencies of these components are consistent with the existence of an extensive antiparallel beta-strand secondary structure. The exchange properties of the amide protons of factor H as measured in 2H2O buffers are rapid and lead to an estimate of NH proton nonexchange that is comparable with those for small globular proteins. Human factor H is constructed from a linear sequence of 20 short consensus repeats with a mean of 61 residues in each one. To investigate the secondary structure further, secondary structure predictions were carried out on the basis of an alignment scheme for 101 sequences for these repeats as found in human factor H and 12 other proteins. These predictions were averaged in order to improve the reliability of the calculations. Both the Robson and the Chou-Fasman methods indicate significant beta-structural contents. Residues 21-51 in the 61-residue repeat show a clear prediction of four strands of beta-structure and four beta-turns. A structural model based on antiparallel beta-strands in the secondary structure is proposed and discussed.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed2005

Study on Angelica and its different extracts by Fourier transform infrared spectroscopy and two-dimensional correlation IR spectroscopy.

In order to develop a rapid and effective analysis method for studying integrally the main constituents in the medicinal materials and their extracts, discriminating the extracts from different extraction process, comparing the categories of chemical constituents in the different extracts and monitoring the qualities of medicinal materials, we applied Fourier transform infrared spectroscopy (FT-IR) associated with second derivative infrared spectroscopy and two-dimensional correlation infrared spectroscopy (2D-IR) to study the main constituents in traditional Chinese medicine Angelica and its different extracts (extracted by petroleum ether, ethanol and water in turn). The findings indicated that FT-IR spectrum can provide many holistic variation rules of chemical constituents. Use of the macroscopical fingerprint characters of FT-IR and 2D-IR spectrum can not only identify the main chemical constituents in medicinal materials and their different extracts, but also compare the components differences among the similar samples. This analytical method is highly rapid, effective, visual and accurate for pharmaceutical research.

Alkanes↗

PubMed2003

Discrimination of Fritillary according to geographical origin with Fourier transform infrared spectroscopy and two-dimensional correlation IR spectroscopy.

Fritillaria is a traditional Chinese herbal medicine for eliminating phlegm and relieving a cough with a long history in China and some other Asian countries. The objective of this study is to develop a nondestructive and accurate method to discriminate Fritillaria of different geographical origins, which is a troublesome work by existing analytical methods. We conducted a systematic study on five kinds of Fritillaria by Fourier transform infrared spectroscopy, second derivative infrared spectroscopy, and two-dimensional (2D) correlation infrared spectroscopy under thermal perturbation. Because Fritillaria consist of a large amount of starch, the conventional IR spectra of different Fritillaria only have very limited spectral feature differences. Based on these differences, we can separate different Fritillaria to a limited extent, but this method was deemed not very practical. The second derivative IR spectra of Fritillaria could enhance spectrum resolution, amplify the differences between the IR spectra of different Fritillaria, and provide some dissimilarity in their starch content, when compared with the spectrum of pure starch. Finally, we applied thermal perturbation to Fritillaria and analyzed the resulting spectra by the 2D correlation method to distinguish different Fritillaria easily and clearly. The distinction of very similar Fritillaria was possible because the spectral resolution was greatly enhanced by the 2D correlation spectroscopy. In addition, with the dynamic information of molecular structure provided by 2D correlation IR spectra, we studied the differences in the stability of active components of Fritillaria. The differences embodied mainly on the intensity ratio of the auto-peak at 985 cm(-1) and other auto-peaks. The 2D correlation IR spectroscopy (2D IR) of Fritillaria can be a new and powerful method to discriminate Fritillaria.

China↗

PubMed1994

Use of photoacoustic Fourier-transform infrared spectroscopy to study phosphates in proteins.

Photoacoustic Fourier-transform infrared spectroscopy was used to study phosphoamino acids and phosphoproteins. Using this method, we have found that the spectral properties of phosphate esters depend on the nature of the linkage, pH, and binding of metal ion. At high pH values, dianionic symmetric stretching of phosphotyrosine and phosphoserine occurs at 984 and 974 reciprocal centimeters, respectively. Analysis of the IR bands of bound phosphate in phosvitin at different pH values gives the pKa value for the esterified phosphates. Addition of aluminum ions to phosvitin at different pH values causes a shift in the phosphate band consistent with a direct binding of aluminum ions to the esterified phosphate. The phosphate signal for 40 micrograms of Pepsin (1 P/mole) is detectable by this method.

Acoustics↗

PubMed2001

Dietary fats affect rat plasma lipoprotein secondary structure as assessed by Fourier transform infrared spectroscopy.

This investigation was undertaken to determine by Fourier transform infrared spectroscopy the effects of diets enriched with fish, sunflower or olive oils on the secondary structure of plasma HDL and LDL from rats, as well as the effects on lipid unsaturation and acyl chain lengths. Controls were fed a commercial diet. In HDL, random coil conformation was relatively high in rats fed the fish diet, probably due to the irregular geometry of polyunsaturated fatty acids interacting with apoproteins. Parallel structural behaviors were observed for rats fed control and olive oil diets. The lowest lipid unsaturation level was found in HDL of rats fed olive oil, and acyl chain lengths were slightly increased by the three fats. Rats fed olive oil had the lowest percentage of LDL beta-sheets and these were more abundant in rats fed the fish oil diet. The least lipid unsaturation in LDL was in rats fed the olive oil diet. No significant differences in acyl chain lengths were observed. Certain protein conformational changes and/or apoprotein composition differences due to dietary fat may affect the binding between lipoproteins and their receptors in cells.

Animals↗

PubMed2001

Assessment of maturity degree of composts from domestic solid wastes by fluorescence and Fourier transform infrared spectroscopies.

Methods of assessment of compost maturity are needed so the application of composted materials to lands will provide optimal benefits. The aim of the present paper is to assess the maturity reached by composts from domestic solid wastes (DSW) prepared under periodic and permanent aeration systems and sampled at different composting time, by means of excitation-emission matrix (EEM) fluorescence spectroscopy and Fourier transform infrared spectroscopy (FT-IR). EEM spectra indicated the presence of two different fluorophores centered, respectively, at Ex/Em wavelength pairs of 330/425 and 280/330 nm. The fluorescence intensities of these peaks were also analyzed, showing trends related to the maturity of composts. The "contour density" of EEM maps appeared to be strongly reduced with composting days. After 30 and 45 days of composting, FT-IR spectra exhibited a decrease of intensity of peaks assigned to polysaccharides and in the aliphatic region. EEM and FT-IR techniques seem to produce spectra that correlate with the degree of maturity of the compost. Further refinement of these techniques should provide a relatively rapid method of assessing the suitability of the compost to land application.

Carbon↗