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PubMed2003

Conformational changes of pediocin in an aqueous medium monitored by fourier transform infrared spectroscopy: a biological implication.

Fourier transform infrared (FTIR) spectroscopy was used to investigate the secondary structure of pediocin PA-1 in different aqueous media in relation to its antimicrobial activity. The experiments were performed at pD (pH meter corrected for deuterium isotope effect) 6, 7, and 8 and during a heating-cooling cycle of 20-80 degrees C. At pD 6, (i.e. pediocin's most active form), the FTIR results show that pediocin adopts an unordered structure with a small contribution of beta-turn. After a heating-cooling cycle, thermally-induced changes in pediocin are reversed and its activity is maintained. Increasing the pD to 7 and 8 leads to a more ordered secondary structure. For these two pD values, an increase in temperature induces an irreversible aggregation of protein as revealed by the amide I' band. The analysis of the Tyr region provides more insight into the aggregation process. In fact, it appears to be a two-step process, involving first the C (carboxy)-terminus of pediocin and then the N (amino)-terminus. This study reveals two major points: (1) the preservation of pediocin flexibility is essential for maintaining its activity; and (2) the aggregation of its C-terminus is sufficient to induce a loss of activity, suggesting that this region plays an important role in the activity of pediocin.

Anti-Bacterial Agents↗

PubMed2006

Quantification of volatile organics in soil aging experiments using fourier transform infrared spectroscopy.

On-line Fourier transform infrared (FT-IR) spectroscopy was applied to monitor the concentration of halogenated volatile organic compounds in a sample-preparation process that simulates long-term, slow accumulation of contaminants in soils (i.e., aging). Artificial aging is conducted by circulating a supercritical fluid solution containing the contaminant(s) of interest through a packed soil column. Mid-infrared spectra of several volatile halocarbons were measured in supercritical Xe and CO(2) to evaluate possible interferences from the strong absorption of CO(2). Although some of the C-X bands were partially masked in supercritical CO(2), all of the compounds studied had distinct spectral features in the region 1400-700 cm(-1) and could be monitored in either solvent. Quantitative measurements of halogenated volatile organics in supercritical CO(2) were demonstrated with CCl(4). Excellent results were obtained over the range 7-280 mM. Representative artificial aging experiments were conducted on two test soils using CCl(4) as the contaminant. On-line (FT-IR) estimates of the aged soil concentrations were 1.3-4.4 times higher than off-line concentrations obtained by gas chromatography/mass spectrometry. The discrepancies were primarily ascribed to post-aging losses that occurred during depressurization and subsequent sample handling. FT-IR spectroscopy is shown to be a powerful tool for monitoring soil loading behavior and for developing artificial aging protocols.

Carbon↗

PubMed2002

Rapid and quantitative detection of the microbial spoilage of meat by fourier transform infrared spectroscopy and machine learning.

Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable "fingerprints." Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 10(7) bacteria.g(-1) the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels.

Artificial Intelligence↗

PubMed2006

Rapid detection and identification of Pseudomonas aeruginosa and Escherichia coli as pure and mixed cultures in bottled drinking water using fourier transform infrared spectroscopy and multivariate analysis.

Fourier transform infrared (FT-IR) spectroscopy and multivariate analysis were used to identify Pseudomonas aeruginosa and Escherichia coli ATCC 25922 inoculated into bottled drinking water. Three inoculation treatments were examined: (i) E. coli ATCC 25922 (N = 3), (ii) P. aeruginosa (N = 3), and (iii) a 1:1 (v:v) mixed culture of both P. aeruginosa and E. coli ATCC 25922 (N = 3). The control treatment was noninoculated drinking water (N = 3). Second derivative transformation and loadings plots over the range of 1800-900 cm(-1) indicate variations in the following bacterial constituents: amide I band ca. 1650 cm(-1), amide II band ca. 1540 cm(-1), phosphodiester backbone of nucleic acids ca. 1242 and 1080 cm(-1), and polysaccharide compounds ca. 1050-950 cm(-1). Cells with the different treatments were clearly segregated from a mean centered principal component analysis. By using soft independent modeling of class analogy analysis, spectra from a given treatment could be correctly classified 83-88% of the time. These results suggest that FT-IR spectroscopy can determine whether a pure culture is present, in addition to confirming that this method can discriminate between closely related bacteria based on differences in biochemical and phenotypic characteristics that can be detected in this spectral region.

Analysis of Variance↗

PubMed2004

Discrimination of intact and injured Listeria monocytogenes by Fourier transform infrared spectroscopy and principal component analysis.

Fourier transform infrared spectroscopy (FT-IR, 4000-600 cm(-)(1)) was used to discriminate between intact and sonication-injured Listeria monocytogenes ATCC 19114 and to distinguish this strain from other selected Listeria strains (L. innocua ATCC 51742, L. innocua ATCC 33090, and L. monocytogenes ATCC 7644). FT-IR vibrational overtone and combination bands from mid-IR active components of intact and injured bacterial cells produced distinctive "fingerprints" at wavenumbers between 1500 and 800 cm(-)(1). Spectral data were analyzed by principal component analysis. Clear segregations of different intact and injured strains of Listeria were observed, suggesting that FT-IR can detect biochemical differences between intact and injured bacterial cells. This technique may provide a tool for the rapid assessment of cell viability and thereby the control of foodborne pathogens.

Food Contamination↗

PubMed1996

Secondary structure of anthrax lethal toxin proteins and their interaction with large unilamellar vesicles: a fourier-transform infrared spectroscopy approach.

Attenuated total reflection Fourier transform infrared spectroscopy has been used to study the secondary structure of anthrax lethal toxin proteins: protective antigen (PA) and lethal factor (LF), as a function of pH in the absence and in the presence of phospholipid vesicles. We first characterized the binding of LF and PA to the lipid membrane and demonstrated the strong pH dependence of the association of PA and LF to the lipid bilayer as well as the effect of pH neutralization on this binding. Binding of LF to the lipid membrane can be, at least partially, reversed when the pH is brought to neutral whereas in the same conditions PA binding is irreversible. Characterization of the conformational changes undergone by PA and LF upon pH lowering, lipid binding, and, in the case of LF, reversal of binding was carried out (i) by determining the secondary structure of the proteins and (ii) by evaluating their ability to undergo an hydrogen/deuterium exchange.

Antigens, Bacterial↗

PubMed1998

Rapid and reliable identification of food-borne yeasts by Fourier-transform infrared spectroscopy.

Computer-based Fourier-transform infrared spectroscopy (FT-IR) was used to identify food-borne, predominantly fermentative yeasts. Dried yeast suspensions provided the films suitable for FT-IR measurement. Informative windows in the spectrum were selected and combined to achieve optimal results. A reference spectrum library was assembled, based on 332 defined yeast strains from international yeast collections and our own isolates. All strains were identified with conventional methods using physiological and morphological characteristics. In order to assess identification quality, another 722 unknown yeast isolates not included in the reference spectrum library were identified both by classical methods and by comparison of their FT-IR spectra with those of the reference spectrum library. Ninety-seven and one-half percent of these isolates were identified correctly by FT-IR. Easy handling, rapid identification within 24 h when starting from a single colony, and a high differentiation capacity thus render FT-IR technology clearly superior to other routine methods for the identification of yeasts.

Cluster Analysis↗

PubMed2003

Measuring enzymatic activity of a recombinant amidase using Fourier transform infrared spectroscopy.

A method based on Fourier transform infrared spectroscopy (FT-IR) has been developed for assaying the Pseudomonas aeruginosa native amidase (E.C. 3.5.1.4), overproduced in an Escherichia coli strain. The kinetic of acetamide hydrolysis by the enzyme, in aqueous media, was monitored by measuring the intensity of the acetamide amide I band maximum at 1635 cm(-1) as a function of time. A value of 0.5mM(-1) cm(-1) was obtained for the extinction coefficient (epsilon) of acetamide at this frequency. The rate of the hydrolysis was found to be linear with the concentration of the enzyme up to 90 microM. The Michaelis-Menten kinetics parameters V and K(m) were determined as 30.7 U/mg and 4mM, respectively. These results were similar to those obtained using high-performance liquid chromatography analysis of the same hydrolytic reaction catalyzed by amidase either in water or in buffer. This suggests that the precision of the FT-IR method is suitable for the kinetic studies of amidase with the additional advantage of being able to perform a real-time measurement of the enzymatic activity.

Acetamides↗

PubMed1996

Membrane fluidity response to odorants as seen by 2H-NMR and infrared spectroscopy.

Fourier transform infrared spectroscopy (FTIR) and deuterium nuclear magnetic resonance spectroscopy (2H-NMR) have been used to study the location of two odorants, beta-ionone and menthone, in a model membrane of dimyristoylphosphatidylcholine, as well as the effect of the odorants on the structure and dynamics of the phospholipids. The interaction has been investigated for two lipid-to-odorant molar ratios, 10:1 and 1:1. The two odorants were found to affect the fluidity of the membrane. More specifically, the 2H-NMR results indicate that at a lipid-to-odorant molar ratio of 10:1, both beta-ionone and menthone increase the order of the deuterons in the interfacial and headgroup regions of the lipid while the incorporation of the odorants at a lipid-to-odorant molar ratio of 1:1 decreases the order of both the lipid headgroup and acyl chains. On the other hand, the infrared results show that the incorporation of beta-ionone and menthone decreases the phase transition temperature and cooperativity of the lipid acyl chains. The results suggest that the site of incorporation of beta-ionone and menthone is very similar in DMPC membranes.

Dimyristoylphosphatidylcholine↗

PubMed2004

[Studied on the identification of Fructus amomi from its confusable varieties by Fourier transform infrared spectroscopy].

This paper uses Fourier transform infrared spectrometer with OMNI sampler to distinguish Fructus amomi from their confusable varieties, i. e. Amomum aurantiacum H. T. Tsai et S. W. Zhao, Amomum chinense Chun ex T. L. Wu, Alpinia chinensis (Ketz.) Rosc and Alpinia japonica (Thunb.) Miq. IRs of Amomum villosum Lour., Amomum longiligulare T. L. Wu and Amomum villosum Lour. Var xanthioides T. L. Wu et Senjen are resemble, and they are markedly different from the FTIR of the confusable varieties. Repeat experiments were processed with different samples of the same set, and the probability is 1.000. The result shows that FTIR can be directly used to distinguish Fructus amomi from their confusable varieties.

Alpinia↗

PubMed1997

Localization and orientation of functional water molecules in bacteriorhodopsin as revealed by polarized Fourier transform infrared spectroscopy.

Linear dichroic difference Fourier transform infrared spectra upon formation of the M photointermediate were recorded with oriented purple membranes. The purpose was to determine the angle of the directions of the dipole moments of 1) the water molecule whose O-H stretching vibration appears at 3643 cm-1 for the unphotolyzed state and 3671 cm-1 for the M intermediate, and 2) the C=O bond of protonated Asp85 in the M intermediate. The angle of 36 degrees we find for the C=O of the protonated Asp85 in the M intermediate is not markedly different from 26 degrees for unprotonated Asp85 in the model based on cryoelectron diffraction, indicating the absence of gross orientation changes in Asp85 upon its protonation. The O-H band at 3671 cm-1 of a water molecule in the M intermediate, although its position has not determined, is fixed almost parallel to the membrane plane. For the unphotolyzed state the angle of the water O-H to the membrane normal was determined to be 60 degrees. On the basis of these data and the structural model, we place the water molecule in the unphotolyzed state at a position where it forms hydrogen bonds with the Schiff base, Asp85, Asp212, and Trp86.

Aspartic Acid↗

PubMed2004

A Fourier-transform infrared spectroscopy study of sugar glasses.

Fourier-transform infrared spectroscopy (FTIR) was used to study the hydrogen-bonding interactions that take place in vitrified carbohydrates of different chain lengths. The band position of the OH stretching band (vOH) and the shift in band position as a function of temperature were determined from the FTIR spectra as indicators for the length and strength of intermolecular hydrogen bonds, respectively. Differential scanning calorimetry (DSC) was used to corroborate the FTIR studies and to measure the change in heat capacity (delta C(p)) that is associated with the glass transition. We found that with increasing T(g), the band position of vOH increases, the wavenumber-temperature coefficient of vOH in the glassy state, WTC(g), increases, whereas (delta C(p) decreases. The positive correlation that was found between vOH and the glass transition temperature, T(g), indicates that the length of the hydrogen bonds increases with increasing T(g). The increase in WTC(g) with increasing T(g) indicates that the average strength of hydrogen bonding decreases with increasing T(g). This implies that oligo- and polysaccharides (high T(g)) have a greater degree of freedom to rearrange hydrogen bonds during temperature changes than monosaccharides (low T(g)). Interestingly, WTC(g) and delta C(p) showed a negative linear correlation, indicating that the change in heat capacity during the glass transition is associated with the strength of the hydrogen-bonding network in the glassy state. Furthermore, we report that introduction of poly-L-lysine in glassy sugar matrices decreases the average length of hydrogen bonds, irrespective of the size of the carbohydrate. Palmitoyl-oleoyl-phosphatidylcholine (POPC) vesicles were found to only interact with small sugars and not with dextran.

1,2-Dipalmitoylphosphatidylcholine↗

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↗

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↗

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↗