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PubMed1987

Changes in the secondary structure of apolipoprotein B-100 after Cu2+-catalysed oxidation of human low-density lipoproteins monitored by Fourier transform infrared spectroscopy.

Fourier transform infrared (FTIR) spectra have been obtained of human low-density lipoproteins (LDL) in H2O and 2H2O buffers. The absorption bands are assigned to vibrations of the lipid and apolipoprotein B-100 components. The analysis of second-derivative spectra allowed an assignment of individual protein bands to alpha-helical, random, coil or beta-structure and beta-turn conformations. Changes in the FTIR spectra after Cu2+-catalysed oxidation of the LDL particles indicate that the structure of apolipoprotein B-100 becomes less ordered, with some alterations of alpha-helical and beta-turn conformation. The main beta-structure absorption at 1620 cm-1 is unaffected by oxidation. Taking into account the resistance to oxidation and the slow H-2H exchange it is suggested that the beta-structure is hidden from external factors whereas other structures are mostly present on the surface of the LDL particle. Oxidation affects mainly the surface region of apolipoprotein B-100 and leads to a structural rearrangement which consequently changes the receptor specificity of the LDL.

Apolipoprotein B-100↗

PubMed1994

Conformational changes upon dissociation of a globular protein from pea: a Fourier transform infrared spectroscopy study.

Fourier transform infrared spectroscopy shows that the secondary structure of legumin, a globular protein from pea seeds, is composed of 41% beta-sheets and 16% alpha-helices and furthermore reveals the presence of beta-turns. The conformation prediction from the analysis of the amino-acid sequence of legumin using hydrophobic cluster analysis reveals that the C-terminal part of the alpha-polypeptide is devoid of defined secondary structures, whereas the beta-polypeptide is highly ordered. Comparison with analogous 11S globulins from other plant families indicates that ordered domains are highly preserved, phenomenon that may be associated with the similarity of the quaternary structure of these proteins. The results also reveal the presence of a large hypervariable region, located at the surface of the protein, that could be at the origin of the different functional properties of the 11S type globulins. The step-by-step destruction of the quaternary oligomeric structure of the native protein is accompanied by conformational changes that depend on the dissociation conditions. Whereas acylation leads to a decrease of the alpha-helix content by 10% at the expense of the beta-sheet content, addition of sodium perchlorate results in the conversion of 10% of the protein secondary structure from beta-sheet to unordered. These observations provide further evidence of the existence of different monomeric states that differ from their secondary structure and, therefore, exhibit different surface-active properties.

Amino Acid Sequence↗

PubMed2006

Detection of Escherichia coli O157:H7 and Salmonella typhimurium using filtration followed by Fourier-transform infrared spectroscopy.

Fourier-transform infrared spectroscopy has been successfully used as a nondestructive method for identifying, distinguishing, and classifying pathogens. In this study, a less time-consuming Fourier-transform infrared procedure was developed to identify Escherichia coli O157:H7 and Salmonella Typhimurium. Samples containing 10(9) CFU/ml were prepared in tryptic soy broth and then serially diluted (up to eight times) to obtain bacterial solutions of 10(9) to 10 CFU/ml. These dilutions were incubated at 37 degrees C for 6 h, samples were filtered through a Metricel filter hourly (for 0 to 6 h), and spectra were obtained using a ZnSe contact attenuated total reflectance accessory on a Continu mum infrared microscope. Midinfrared spectra (4,000 to 700 cm(-1)) of Salmonella Typhimurium and E. coli O157:H7 were generated, and peak areas in the region of 1,589 to 1,493 cm(-1) were used to detect the pathogens. Initially, detection limits were between 10(6) and 10(7) CFU/ml without preenrichment, and samples starting with 500 CFU/ml were detectable following incubation for 6 h, when counts reached at least 10(6) CFU/ ml. Compared with results of previously published studies in which Fourier-transform infrared spectroscopy was used to identify select pathogens, this method is more rapid and less expensive for practical large-scale sample analysis.

Colony Count, Microbial↗

PubMed2004

Taxonomic discrimination of flowering plants by multivariate analysis of Fourier transform infrared spectroscopy data.

Fourier transform infrared spectroscopy (FTIR) provides biochemical profiles containing overlapping signals from a majority of the compounds that are present when whole cells are analyzed. Leaf samples of seven higher plant species and varieties were subjected to FTIR to determine whether plants can be discriminated phylogenetically on the basis of biochemical profiles. A hierarchical dendrogram based on principal component analysis (PCA) of FTIR data showed relationships between plants that were in agreement with known plant taxonomy. Genetic programming (GP) analysis determined the top three to five biomarkers from FTIR data that discriminated plants at each hierarchical level of the dendrogram. Most biomarkers determined by GP analysis at each hierarchical level were specific to the carbohydrate fingerprint region (1,200-800 cm(-1)) of the FTIR spectrum. Our results indicate that differences in cell-wall composition and structure can provide the basis for chemotaxonomy of flowering plants.

Biomarkers↗

PubMed2005

Analysis of organic acids in wines by Fourier-transform infrared spectroscopy.

Fourier-transform infrared (FTIR) spectroscopy has been a major point of development in many wine laboratories in recent years. It enables almost instant analysis of several properties of wine, usually with very good precision and accurate results. Nevertheless, validation procedures should not be forgotten and should be fully performed. Recovery experiments were performed by spiking wine samples with different amounts of organic acids (tartaric, malic, lactic, acetic and citric--the most prominent in wines). After FTIR analysis of the total acidity and of each organic acid concentration, recoveries were calculated. For total acidity recovery results were, in general, good and very close to 100% (64-111%). On the other hand, for individual organic acid concentrations, the recovery results were lower than 100% (11-73%) for all spiking additions. These results could be explained by spectroscopic interferences between the organic acids. Because they have similar infrared spectra, it is not easy to distinguish between them and, therefore, to achieve accurate calibration. When total acidity, with a different infrared spectrum from the other abundant compounds in the wine, was taken as a single property the recovery results were acceptable.

Acids↗

PubMed2003

Monitoring of apoptosis of HL60 cells by Fourier-transform infrared spectroscopy.

Fourier-transform infrared (FTIR) spectroscopy is a vibrational technique that gives information on the chemical composition of a sample, providing a "molecular fingerprint" of it. It is a powerful approach to study intact cells. The aim of the present study was to analyse and quantify apoptotic cells by using a FTIR approach based on attenuated total reflection (ATR). We incubated human HL60 leukaemic cells with camptothecin, a cytotoxic drug, and monitored apoptosis induction over a period of time. Several ATR-FTIR spectral changes occurred during the apoptotic process. In particular, we observed that the apoptotic index was inversely correlated with the spectral area in the region 1200-900 cm(-1), assigned to the absorption of nucleic acids. We therefore propose that ATR-FTIR spectral features may be used as a diagnostic marker of apoptotic cells.

Amino Acid Chloromethyl Ketones↗

PubMed1986

Orientation measurements on ordered multibilayers of phospholipids and sphingolipids from synthetic and natural origin by ATR Fourier transform infrared spectroscopy.

Fourier-transform infrared spectroscopy was applied to natural and synthetic planar membrane multibilayer systems made from phospholipids and sphingolipids to perform orientational measurements utilizing the attenuated total reflectance technique. Applying polarized infrared light, the dichroic ratios and the positions of the peak maxima of various infrared-active bands in dependence on temperature and degree of hydration as well as the phase behaviour were studied. Under certain assumptions - which are discussed - made for the order parameter S, the orientation of various functional groups with respect to the molecular axis or to the membrane normal can be determined. For the gel phase values for S between 0.80 +/- 0.05 for the complete molecule and 0.40 +/- 0.05 for the end methyl group and for the liquid crystalline phase a value of 0.50 +/- 0.05 were approximated. Applying these data, a relatively precise determination of the angles of the oscillating dipole moments of various functional groups could be performed, which - for some vibrations - deviate considerably from those angles assumed earlier. Regarding the phase behaviour, it was found that not only the degree of hydration but the amount of bulk water of the sample has a strong influence on the phase transition temperature Tc (lyotrophism), but only a weak influence on the orientational data.

Fourier Analysis↗

PubMed1989

Structure of cytochrome b5 in solution by Fourier-transform infrared spectroscopy.

Fourier-transform infrared spectroscopy was used to examine the secondary structure of rabbit liver cytochrome b5 and the polar and nonpolar domains of the protein. The data for both the polar and nonpolar domains agree well with those previously obtained by other physical techniques. In particular it was found that the nonpolar membrane-binding domain was predominantly alpha helix and that the polar domain was also highly helical, but not all alpha helix. The independence of the two domains in the whole molecule was, in general, confirmed by the additivity of the spectra of the two domains. The small differences that were seen indicate that there is a loss of alpha helix when the protein is cut into the two domains. In addition, there appeared to be a slight difference in the exposure to solvent of the amide NH groups in the alpha-helical portion of the nonpolar domain when it was examined in isolation.

Animals↗

PubMed1990

Topography of the membrane-binding domain of cytochrome b5 in lipids by Fourier-transform infrared spectroscopy.

Fourier-transform infrared spectroscopy was used to examine the secondary structure of the membrane-binding domain (nonpolar peptide) of rabbit liver cytochrome b5 in D2O and in the presence of phospholipids and deoxycholate. In all situations, the predominant structure was alpha helix, but an examination of the components of the amide I band in the spectrum of the nonpolar peptide showed that the major peak was shifted from 1655 cm-1 in the lipids to 1650 cm-1 in deoxycholate. This shift to lower frequency, together with a decrease in intensity of the amide II band, is indicative of N-H to N-D exchange of the peptide backbone. A semiquantitative analysis indicated that the alpha helix of the peptide is over 95% exchanged in the presence of deoxycholate but is only 10% exchanged in the presence of lipid. These data suggest that the membrane-inserted portion of the peptide is alpha helical and is largely protected from N-H to N-D exchange by the bilayer. We suggest that this technique appears to provide a general method for determining the type of secondary structure involved in membrane interaction and the percentage of this structure which is involved in the interaction.

Amino Acid Sequence↗

PubMed2005

Diagnosis of gastric inflammation and malignancy in endoscopic biopsies based on Fourier transform infrared spectroscopy.

BACKGROUND: Fourier transform infrared (FT-IR) spectroscopy is an effective tool for investigation of chemical changes at the molecular level. We previously demonstrated that FT-IR spectroscopy can reliably distinguish multiple types of carcinoma from healthy tissue. Because various stomach diseases are common, it is important to explore a noninvasive and rapid method to detect malignancy and gastritis in endoscopic biopsies. Our aim was to classify endoscopic biopsies into healthy, gastritis, and malignancy through the use of FT-IR spectroscopy. METHODS: A total of 103 endoscopic samples, including 19 cases of cancer, 35 cases of chronic atrophic gastritis, 29 cases of chronic superficial gastritis, and 20 healthy tissue samples, were obtained at the First Hospital of Xi'an Jiaotong University, China. A modified attenuated total reflectance accessory was linked to a WQD-500 FT-IR spectrometer for biopsy measurement. The spectral characteristics for different types of tissues were correlated with the corresponding pathology results. The gastric biopsies were classified by FT-IR spectroscopy and a discriminant analysis method. RESULTS: There were significant differences in the FT-IR spectra of four types of gastric biopsies. The discriminant analysis results demonstrated that the sensitivity of FT-IR detection for healthy, superficial gastritis, atrophic gastritis, and gastric cancer was 90%, 90%, 66%, 74%, respectively, which could help satisfy clinical diagnostic requirements. CONCLUSION: FT-IR spectroscopy can distinguish disease processes in gastric endoscopic biopsies.

Biopsy↗

PubMed2004

The rapid identification of Acinetobacter species using Fourier transform infrared spectroscopy.

AIMS: Fourier transform infrared (FT-IR) was used to analyse a selection of Acinetobacter isolates in order to determine if this approach could discriminate readily between the known genomic species of this genus and environmental isolates from activated sludge. METHODS AND RESULTS: FT-IR spectroscopy is a rapid whole-organism fingerprinting method, typically taking only 10 s per sample, and generates 'holistic' biochemical profiles (or 'fingerprints') from biological materials. The cluster analysis produced by FT-IR was compared with previous polyphasic taxonomic studies on these isolates and with 16S-23S rDNA intergenic spacer region (ISR) fingerprinting presented in this paper. FT-IR and 16S-23S rDNA ISR analyses together indicate that some of the Acinetobacter genomic species are particularly heterogeneous and poorly defined, making characterization of the unknown environmental isolates with the genomic species difficult. CONCLUSIONS: Whilst the characterization of the isolates from activated sludge revealed by FT-IR and 16S-23S rDNA ISR were not directly comparable, the dendrogram produced from FT-IR data did correlate well with the outcomes of the other polyphasic taxonomic work. SIGNIFICANCE AND IMPACT OF THE STUDY: We believe it would be advantageous to pursue this approach further and establish a comprehensive database of taxonomically well-defined Acinetobacter species to aid the identification of unknown strains. In this instance, FT-IR may provide the rapid identification method eagerly sought for the routine identification of Acinetobacter isolates from a wide range of environmental sources.

Acinetobacter↗

PubMed1984

Solvent denaturation of proteins as observed by resolution-enhanced Fourier transform infrared spectroscopy.

Fourier self-deconvolution of Fourier transform infrared (FTIR) spectra and second derivative FTIR spectroscopy were applied to study solvent-induced conformational changes in globular proteins. For beta-lactoglobulin a total of three different denatured forms were identified in alkaline solution and in aqueous methanol-d1 and isopropanol-d1. In isopropanol-d1 solution a new conformation was identified which appears to resemble, but is not identical with, the beta-structure of native proteins. This conformation is characterized by absorption bands around 1615-1618 and 1684-1688 cm-1, and is also observed for concanavalin A and chymotrypsinogen A in aqueous isopropanol-d1 solution.

Animals↗

PubMed1995

Molecular interactions of the redox-active accessory chlorophyll on the electron-donor side of photosystem II as studied by Fourier transform infrared spectroscopy.

A Fourier transform infrared (FTIR) difference spectrum upon photooxidation of the accessory chlorophyll (Chlz) of photosystem II (PS II) was obtained at 210 K with Mn-depleted PS II membranes in the presence of fericyanide and silicomolybdate. The observed Chlz+/Chlz spectrum showed two differential bands at 1747/1736 and 1714/1684 cm-1. The former was assigned to the free carbomethoxy C = 0 and the latter to the keto C = 0 that is hydrogen-bonded or in a highly polar environment. Also, the negative 1614 cm-1 band assignable to the macrocycle mode indicated 5-coordination of the central Mg. The negative 1660 cm-1 band, possibly due to the strongly hydrogen-bonded keto C = 0, may suggest oxidation of one more Chlz, although an alternative assignment, the amide I mode of proteins perturbed by Chlz oxidation, is also possible.

Cell Membrane↗

PubMed1994

Analysis of Fusarium mycotoxins by gas chromatography--Fourier transform infrared spectroscopy.

The Fourier transform infrared (FTIR) spectra of selected Fusarium mycotoxins of various structure types were determined. Absorptions were observed for the following functionalities: hydroxyl at 3625-65 cm-1 and 3482 cm-1, the latter being associated with a 7 alpha-hydroxyl adjacent to an 8-carbonyl in keto trichothecenes; carbonyl at 1760-6 cm-1 for 5-membered rings and at 1695-8 cm-1 for those conjugated to a single C = C in a six-membered ring; acetate carbonyl at 1765 cm-1 and acetate C-O at 1220-9 cm-1; and C = C at 1680 cm-1. Gas chromatography combined with FTIR and mass spectrometry was applied to the identification of some mycotoxins in a F. roseum liquid culture extract.

Chromatography, Gas↗

PubMed1998

Examination of full fat and reduced fat Cheddar cheese during ripening by Fourier transform infrared spectroscopy.

The Fourier transform infrared spectra of reduced fat Cheddar cheese and full fat Cheddar cheese during ripening were examined. A suitable sampling procedure was used to obtain the spectra of cheese samples. The spectra were affected by the moisture contents of the samples, but this effect could be eliminated by equilibration of the sample for at least 10 min before data collection. Strong and well-separated bands at 1744, 1450, 1240, 1170, and 1115 cm-1 arising from fat were observed in the frozen samples. The bands observed at 1650 and 1540 cm-1 were attributed to the protein contents of the cheese samples. The absorption intensities of protein and fat bands corresponded to the amounts of protein and fat that were present in the samples. Distinct changes in the bands of fat and protein of reduced fat and full fat cheese samples occurred during ripening. This technique could provide a basis for a rapid characterization and determination of the age of cheese undergoing ripening.

Caseins↗

PubMed1993

Water structural changes in lumirhodopsin, metarhodopsin I, and metarhodopsin II upon photolysis of bovine rhodopsin: analysis by Fourier transform infrared spectroscopy.

Difference Fourier transform infrared spectra of lumirhodopsin, metarhodopsin I, and metarhodopsin II versus rhodopsin were recorded with hydrated films of bovine rod outer segments at 200, 240, and 270 K. In the region between 3700 and 3450 cm-1, the O-H stretching vibrational bands of water were identified by H(2)18O and 2H2O shifts. Lumirhodopsin and metarhodopsin I exhibit almost identical spectral shape in this region. The O-H stretching vibration band of water was detected at 3533 cm-1 upon formation of lumirhodopsin and metarhodopsin I and at 3641 cm-1 upon formation of metarhodopsin II. The results suggest that hydrogen bonding of water molecules in the protein is stronger in lumirhodopsin and metarhodopsin I, intermediates with a protonated Schiff base, than in metarhodopsin II with an unprotonated Schiff base. This is similar to the case of photoreaction of bacteriorhodopsin, in which stronger hydrogen bonding of water is formed in the L intermediate than the M intermediate [Maeda, A., Sasaki, J., Shichida, Y., & Yoshizawa, T. (1992) Biochemistry 31, 462-467].

Animals↗

PubMed1999

Rovibrational Constants for the nu(6) and 2nu(9) Bands of HCOOD by Fourier Transform Infrared Spectroscopy.

The Fourier transform infrared spectrum of the nu(6) and 2nu(9) bands of deuterated formic acid (HCOOD) was recorded with an apodized resolution of 0.004 cm(-1) in the frequency range of 930-1040 cm(-1). These two bands with band centers 40 cm(-1) apart were mutually coupled by Coriolis and Fermi interactions. By fitting a total of 1076 infrared transitions of both nu(6) and 2nu(9) with a standard deviation of 0.00075 cm(-1) using a Watson's A-reduced Hamiltonian in the I(r) representation with the inclusion of c-type Coriolis and a Fermi-resonance term, two sets of rovibrational constants for v(6) = 1, and v(9) = 2 states were derived for the first time. Both nu(6) and 2nu(9) bands are A type with band centers at 972.8520 +/- 0.0001 and 1011.6766 +/- 0.0001 cm(-1), respectively. Copyright 1999 Academic Press.

Journal Article↗

PubMed1988

The secondary structure of apolipoproteins in human HDL3 particles after chemical modification of their tyrosine, lysine, cysteine or arginine residues. A Fourier transform infrared spectroscopy study.

Fourier transform infrared spectra of apolipoprotein E-depleted human HDL3 have been obtained in H2O and 2H2O buffers. The absorption bands in the protein amide I and amide II regions (1700-1500 cm-1) were assigned to alpha-helical, disordered and beta-strand/beta-turn structures of apolipoproteins A-I and A-II (apoA-I and apoA-II), the apolipoprotein constituents of HDL3. Modification of HDL3 by tetranitromethane (TNM) treatment, acetylation, reduction plus alkylation and 1,2-cyclohexanedione treatment derivatised tyrosine, lysine, cysteine and arginine residues, respectively, and caused alteration of the secondary structure of the HDL3 apolipoproteins to different extents. Each of the chemical modifications caused changes in the frequency of bands associated with beta-strands/beta-turns, but only TNM treatment of HDL3, as judged by the second- and fourth-derivative spectra, resulted in a shift of the band assigned to the alpha-helical structure of the proteins. In agreement with other workers, only TNM treatment of HDL3 particles was found to inhibit their binding by high-affinity cell membrane receptors. It is proposed, therefore, that receptor recognition of HDL3 particles is dependent on conservation of the alpha-helix structures within apoA-I and apoA-II, and that beta-strand/beta-turn structures are not involved. This conclusion is consistent with the predominance of amphipathic alpha-helical structures in both apolipoproteins and with the relaxed specificity of the receptors which are thought to recognise both apoA-I and apoA-II.

Acylation↗