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Results for “Spectroscopy, Fourier Transform Infrared”

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PubMed2004

High-throughput metabolic fingerprinting of legume silage fermentations via Fourier transform infrared spectroscopy and chemometrics.

Silage quality is typically assessed by the measurement of several individual parameters, including pH, lactic acid, acetic acid, bacterial numbers, and protein content. The objective of this study was to use a holistic metabolic fingerprinting approach, combining a high-throughput microtiter plate-based fermentation system with Fourier transform infrared (FT-IR) spectroscopy, to obtain a snapshot of the sample metabolome (typically low-molecular-weight compounds) at a given time. The aim was to study the dynamics of red clover or grass silage fermentations in response to various inoculants incorporating lactic acid bacteria (LAB). The hyperspectral multivariate datasets generated by FT-IR spectroscopy are difficult to interpret visually, so chemometrics methods were used to deconvolute the data. Two-phase principal component-discriminant function analysis allowed discrimination between herbage types and different LAB inoculants and modeling of fermentation dynamics over time. Further analysis of FT-IR spectra by the use of genetic algorithms to identify the underlying biochemical differences between treatments revealed that the amide I and amide II regions (wavenumbers of 1,550 to 1,750 cm(-1)) of the spectra were most frequently selected (reflecting changes in proteins and free amino acids) in comparisons between control and inoculant-treated fermentations. This corresponds to the known importance of rapid fermentation for the efficient conservation of forage proteins.

Fabaceae↗

PubMed2006

Assignment of the vibrational modes of the chromophores of iodopsin and bathoiodopsin: low-temperature fourier transform infrared spectroscopy of 13C- and 2H-labeled iodopsins.

To investigate the chromophore structures of iodopsin and its low-temperature photoproducts, we have assigned their vibrational bands in the Fourier transform infrared (FTIR) spectra using iodopsin samples that were reconstituted with a series of (13)C- and deuterium-labeled retinals. The analyses of the vibrational bands in the fingerprint and hydrogen-out-of-plane (HOOP) regions indicated that the structure of the chromophores in the iodopsin system differs near their centers from those in the rhodopsin system. Compared to rhodopsin, the chromophore of the batho intermediate of iodopsin is twisted in the C(12) to C(14) regions but is more planar around C(11) region. The large amount of twisting was reduced by removing the chloride ion from the iodopsin, suggesting that this twisting hinders the relaxation of the torsion near C(11) necessary for the transition to the lumi intermediate and thus results in the thermal reversion of the batho intermediate back to the iodopsin. From the analyses of the C=NH and C=ND stretching bands, we conclude that the displacement of the Schiff base region upon photoisomerization of the chromophore is restricted, as is the case for rhodopsin. These results indicated that iodopsin's chromophore has a unique structure near its center and that this difference is enhanced by the binding of chloride nearby.

Chlorides↗

PubMed1999

Pressure-induced conformational changes of beta-lactoglobulin by variable-pressure Fourier transform infrared spectroscopy.

Pressure-induced conformational changes in D(2)O solutions of the two genetic variants of beta-lactoglobulin A (beta-lg A) and beta-lactoglobulin B (beta-lg B) and an equal mixture of both variants (beta-lg A+B) were studied by employing variable-pressure Fourier transform infrared (VP-FTIR) spectroscopy. Changes in the secondary structure of beta-lg A were observed at lower pressure compared to beta-lg B, indicating that beta-lg A had a more flexible structure. During the decompression cycle beta-lg A showed protein aggregation, accompanied by an increase in alpha-helical conformation. The changes in the secondary structure of beta-lg B with the pressure were minor and for the most part reversible. Upon decompression no aggregation in beta-lg B was observed. Increasing the pressure from 0.01 to 12.0 kbar of a solution containing beta-lg A+B resulted in substantial broadening of all major amide I bands. This effect was partially reversed by decreasing the hydrostatic pressure. beta-lg A+B underwent less aggregate formation than beta-lg A, possibly as a result of protein-protein interactions between beta-lg A and beta-lg B. Hence, it is likely that the functional or biological attributes of beta-lg proteins may be affected in different ways by hydrostatic pressure.

Deuterium↗

PubMed1997

Fourier transform infrared spectroscopy study of the secondary structure of the gastric H+,K+-ATPase and of its membrane-associated proteolytic peptides.

Membrane topology of the H+,K+-ATPase has been studied after proteolytic degradation of the protein by proteinase K. Proteinase K had access to either the cytoplasmic part of the protein or to both sides of the membrane. Fourier transform infrared attenuated total reflection spectroscopy indicated that membrane-associated domain of the protein represented about 55% of the native protein, meanwhile the cytoplasmic part represented only 27% of the protein. The secondary structure of the ATPase and of its membrane-associated domains was investigated by infrared spectroscopy. The secondary structure of the membrane-associated structures and of the entire protein was quite similar (alpha-helices, 35%; beta-sheets, 35%; turns, 20%; random, 15%). These data were in agreement with 10 alpha-helical transmembrane segments but suggested a participation of beta-sheet structures in the membrane-associated part of the protein. Polarized infrared spectroscopy indicated that the alpha-helices were oriented nearly perpendicular to the membrane plane. No preferential orientation could be attributed to the beta-sheets. Monitoring the amide hydrogen/deuterium exchange kinetics demonstrated that the membrane associated part of the ATPase molecule is characterized by a relatively high accessibility to the solvent, quite different from that observed for bacteriorhodopsin membrane segments.

Animals↗

PubMed2006

Interactions involved in the realignment of membrane-associated helices. An investigation using oriented solid-state NMR and attenuated total reflection Fourier transform infrared spectroscopies.

A series of histidine-containing peptides (LAH4X6) was designed to investigate the membrane interactions of selected side chains. To this purpose, their pH-dependent transitions from in-plane to transmembrane orientations were investigated by attenuated total reflection Fourier transform infrared and oriented solid-state NMR spectroscopies. Peptides of the same family have previously been shown to exhibit antibiotic and DNA transfection activities. Solution NMR spectroscopy indicates that these peptides form amphipathic helical structures in membrane environments, and the technique was also used to characterize the pK values of all histidines in the presence of detergent micelles. Whereas one face of the amphipathic helix is clearly hydrophobic, the opposite side is flanked by four histidines surrounding six leucine, alanine, glycine, tryptophan, or tyrosine residues, respectively. This diversity in peptide composition causes pronounced shifts in the midpoint pH of the in-plane to transmembrane helical transition, which is completely abolished for the peptides carrying the most hydrophilic amino acid residues. These properties open up a conceptually new approach to study in a quantitative manner the hydrophobic as well as specific interactions of amino acids in membranes. Notably, the resulting scale for whole residue transitions from the bilayer interface to the hydrophobic membrane interior is obtained from extended helical sequences in lipid bilayers.

Alanine↗

PubMed2005

Rapid monitoring of diabetes-induced lipid peroxidation by Fourier transform infrared spectroscopy: evidence from rat liver microsomal membranes.

Increased oxidative stress is the consequence of either enhanced reactive oxygen species (ROS) production or attenuated ROS scavenging capacity, resulting in tissue damage that in most instances is assessed by the measurement of lipid peroxides. In the current study, diabetes-induced lipid peroxidation in rat liver microsomal membranes was investigated by Fourier transform infrared (FT-IR) spectroscopy at different temperatures. The olefinic (CH) band at 3012 cm-1 was used to probe diabetes-induced lipid peroxidation. The intensity and area values of this band of diabetic samples were found to be increased significantly (P<0.05) compared with nondiabetic samples. The increase in olefinic band intensity is attributed mainly to the lipid peroxidation end products. The results of the FT-IR study were found to be in agreement with biochemical studies that revealed a significant increase in malondialdehyde levels of diabetic samples compared with control samples (P<0.05) using the thiobarbituric acid test.

Animals↗

PubMed1995

Fourier transform infrared spectroscopy study of the secondary structure of the reconstituted Neurospora crassa plasma membrane H(+)-ATPase and of its membrane-associated proteolytic peptides.

We reconstituted purified plasma membrane H(+)-ATPase from Neurospora crassa into soybean phospholipid vesicles (lipid/ATPase ratio of 5:1 w/w). The proteoliposomes contained an active ATPase, oriented inside-out. They were subjected to proteolysis by using Pronase, proteinase K, trypsin, and carboxypeptidase Y. Fourier transform infrared attenuated total reflection spectroscopy indicates that the amount of protein remaining after hydrolysis and elimination of the extramembrane domain of ATPase represents about 43% of the intact protein. The secondary structure of intact ATPase and of the membrane-associated domain of ATPase was determined by infrared spectroscopy. The membrane domain shows a typical alpha-helix and beta-sheet absorption. Polarized infrared spectroscopy reveals that the orientation of the helices is about perpendicular to the membrane. Amide hydrogen/deuterium exchange kinetics performed for the intact H(+)-ATPase and for the membrane-associated domain demonstrate that this part of ATPase shows less accessibility to the solvent than the entire protein but remains much more accessible to the solvent than bacteriorhodopsin membrane segments.

Bacteriorhodopsins↗

PubMedDate not supplied

Computer-aided screening for hallucinogenic and stimulant amphetamines with gas chromatography-Fourier transform infrared spectroscopy (GC-FTIR).

An expert system applied as a screening test for amphetamine analogues found in recreational-drug exhibits (tablets or powders) is described. The knowledge base defining the reference Fourier transform infrared spectroscopic (FTIR) spectral patterns has been built according to criteria encompassing toxicological, pharmacological, and neurochemical aspects. The class identity of a compound is determined within seconds using soft independent modeling of class analogy (SIMCA). The predictive value of the system, as assessed at a testing accuracy of 95%, is expressed by a total correct classification rate of 93.93% and by a 96.30% rate of true-positive amphetamines. The specificity and the selectivity of the screening test, evaluated by testing 159 toxicologically relevant compounds, are discussed, emphasizing the chemical and physical factors affecting these parameters. Medicinal amphetamines giving cross-reactions with traditional screening techniques produce a negative result. The specificity of the system characterizes the expert system as a highly sensitive, selective, fast, and user-friendly screening test that screens for amphetamines with prediction accuracy adequate for investigations in analytical toxicology.

Amphetamines↗

PubMed2005

Etching behavior of silicon nanowires with HF and NH4F and surface characterization by attenuated total reflection Fourier transform infrared spectroscopy: similarities and differences between one-dimensional and two-dimensional silicon surfaces.

A systematic study of the etching behavior of one-dimensional (1-D) Si nanowires (SiNWs) in various HF and NH4F etching solutions is reported. The concentration and pH dependences of the etching time (which is inverse to the "stability") of the SiNWs in these solutions were investigated. A V-shaped bimodal etching curve was observed for HF solutions with concentrations of 0.5-40%. Specifically, SiNWs exhibit high stability in both low (0.5%) and high (40%) concentrations of HF solution, with the lowest stability (i.e., fastest etching rate) occurring at 2% (1 M) HF solution. With NH4F, the time needed to totally etch away the SiNWs sample decreases with increasing concentration (from 1-40%). The opposite is true when the pH of the NH4F solution was maintained at 14. These surprising results were rationalized in terms of "passivation" of the SiNW surfaces by HF or related molecules via hydrogen bonding for Si-H-terminated surfaces in HF solutions (with low pH values) and by NH4(+) ions via ionic bonding for Si-O(-)-terminated surfaces in NH4F solutions (with high pH values), respectively. Furthermore, it was found that SiNWs are stable only in relatively narrow pH ranges in these solutions. When SiNWs are etched with HF, the stability range is pH = 1-2 where the surface moieties are Si-H(x) species (x = 1-3). When SiNWs are etched with NH4F, the stability range is pH = 12-14 where the surface moieties are mainly Si-(O-)x species (x = 1-3). These rationales were confirmed by attenuated total reflection Fourier transform infrared spectroscopy measurements, which showed that, while etching SiNWs with HF gave rise to Si-H(x) surface species, no Si-H(x) species were observed when SiNWs were etched with NH4F. The latter finding is at odds with the corresponding results reported for the two-dimensional (2-D) Si wafers where etching with either HF or NH4F produces Si-H(x) species on the surface. This difference suggests either that the etching mechanisms for NH4F versus HF are different for SiNWs or, more likely, that the Si-H(x) surface species produced in NH4F solutions are so unstable that they are hydrolyzed readily at pH > 4. The similarities and differences of the etching behaviors and the resulting surface speciations between the 1-D SiNWs and the 2-D Si wafers suggest that the nanoscale structures as well as the low dimensionality of SiNWs may have contributed to the rapid hydrolysis of the surface Si-H(x) species in NH4F solutions, especially at high pH values.

Journal Article↗

PubMed2005

Generation and characterization of the selenocysteinyl radical: direct evidence from time-resolved UV/Vis, electron paramagnetic resonance, and Fourier transform infrared spectroscopy.

The selenocysteinyl radical 1 has been generated for the first time by laser flash photolysis (lambda(exc) = 266 nm) of dimethyl bis(N-tert-butoxycarbonyl)-l-selenocystine 2 and of [(9-fluorenylideneamino)oxycarbonyl]methyl(N-tert-butoxycarbonyl)-l-selenocysteine 3 in acetonitrile and characterized by time-resolved (TR) UV/Vis, Fourier transform infrared (FTIR), and electron paramagnetic spectroscopy in combination with theoretical methods. A detailed product study was conducted using gas chromatography and one- and two-dimensional NMR spectroscopy. In the case of [(9-fluorenylideneamino)oxycarbonyl]methyl(N-tert-butoxycarbonyl)-l-selenocysteine 3, the (9-fluorenylideneamino)oxycarbonyl moiety serves as a photolabile protection group providing a "caged selenocysteinyl radical" suitable for biophysical applications. Cleavage of the diselenide bridge or the selenium-carbonyl bond by irradiation is possible in high quantum yields. Because of the lack of a good IR chromophore in the mid-IR region, the selenocysteinyl radical 1 cannot be monitored directly by TR FTIR spectroscopy. TR UV/Vis spectroscopy revealed the formation of the selenocysteinyl radical 1 from both precursors. The selenocysteinyl radical 1 has a lifetime tau approximately 63 mus and exhibits a strong band located at lambda(max) = 335 nm. Calculated UV absorptions of the selenocysteinyl radical (UB3LYP/6-311G(d,p)) are in good agreement with the experimental results. The use of TR UV/Vis spectroscopy permitted the determination of the decay rates of the selenocysteinyl radical in the presence of two quenchers. The product studies demonstrated the reversible photoreaction of dimethyl bis(N-tert-butoxycarbonyl)-l-selenocystine 2. Products of the photolysis of the "caged selenocysteinyl radical" precursor 3 are dimethyl bis(N-tert-butoxycarbonyl)-l-selenocystine 2, carbon dioxide, and some further smaller fragments. In addition, the photodecomposition of the (9-fluorenylideneamino)oxycarbonyl moiety produced 9-fluorenone-oxime 4, 9-fluoren-imine 5, and 6 and 7 as products of the dimerization of two 9-fluorenoneiminoxy radicals 8.

Electron Spin Resonance Spectroscopy↗

PubMed1991

Fourier-transform infrared spectroscopy study of dioleoylphosphatidylcholine and monooleoylglycerol in lamellar and cubic liquid crystals.

The liquid-crystalline phases of the systems monooleoylglycerol (MO)/water, dioleoylphosphatidylcholine (DOPC)/water, and MO/DOPC/water have been studied by Fourier-transform infrared (FTIR) spectroscopy. In the latter ternary system, the sn-3 OH group of MO competes with water to interact with the polar head group of DOPC, and an intramolecular hydrogen bonding of MO is broken up. The hydration of the ester carbonyl groups in the lamellar phases of both the MO/water and DOPC/water systems increases with increasing water content. Similarly, the addition of small amounts either of MO to a DOPC/water system or of DOPC to an MO/water system also results in an increase in the hydration of the ester carbonyl groups. This leads to an unfavorable hydrocarbon-water contact which is counteracted by the formation of a cubic phase, except for the DOPC/water system, where the lamellar phase is stable also at the highest water concentrations. The phase behavior of the different systems can be described in terms of lipid monolayer curvature and molecular packing in the lipid aggregates. Finally, it is shown by the water association band in the FTIR spectrum that the water hydrogen bonding is considerably different in the liquid-crystalline phases than in bulk water.

Fourier Analysis↗

PubMed1999

Effects of subunit I mutations on redox-linked conformational changes of the Escherichia coli bo-type ubiquinol oxidase revealed by Fourier-transform infrared spectroscopy.

Cytochrome bo is the heme-copper terminal ubiquinol oxidase in the aerobic respiratory chain of Escherichia coli, and functions as a redox-coupled proton pump. As an extension to our mutagenesis and Fourier-transform infrared studies on ion pumps, we examined the effects of subunit I mutations on redox-linked protein structural changes in cytochrome bo. Upon photo-reduction in the presence of riboflavin, Y288F and H333A showed profound effects in their peptide backbone vibrations (amide-I and amide-II), probably due to the loss of CuB or replacement of high-spin heme o with heme B. In the frequency region of protonated carboxylic C=O stretching vibrations, negative 1,743 cm-1 and positive 1,720 cm-1 bands were observed in the wild-type; the former shifted to 1,741 cm-1 in E286D but not in other mutants including D135N. This suggests that Glu286 in the D-channel is protonated in the air-oxidized state and undergoes hydrogen bonding changes upon reduction of the redox metal centers. Two pairs of band shifts at 2,566 (+)/2,574 (-) and 2,546 (+)/2,556 (-) cm-1 in all mutants indicate that two cysteine residues not in the vicinity of the metal centers undergo redox-linked hydrogen bonding changes. Cyanide had no effect on the protein structural changes because of the rigid local protein structure around the binuclear center or the presence of a ligand(s) at the binuclear center, and was released from the binuclear center upon reduction. This study establishes that cytochrome bo undergoes unique redox-linked protein structural changes. Localization and time-resolved analysis of the structural changes during dioxygen reduction will facilitate understanding of the molecular mechanism of redox-coupled proton pumping at the atomic level.

Binding Sites↗

PubMed1996

Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban.

Phospholamban is a 52-amino acid residue membrane protein that regulates Ca(2+)-ATPase activity in the sarcoplasmic reticulum of cardiac muscle cells. The hydrophobic C-terminal 28 amino acid fragment of phospholamban (hPLB) anchors the protein in the membrane and may form part of a Ca(2+)-selective ion channel. We have used polarized attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy along with site-directed isotope labeling to probe the local structure of hPLB. The frequency and dichroism of the amide I and II bands appearing at 1658 cm-1 and 1544 cm-1, respectively, show that dehydrated and hydrated hPLB reconstituted into dimyristoylphosphatidycholine bilayer membranes is predominantly alpha-helical and has a net transmembrane orientation. Specific local secondary structure of hPLB was probed by incorporating 13C at two positions in the protein backbone. A small band seen near 1614 cm-1 is assigned to the amide I mode of the 13C-labeled amide carbonyl group(s). The frequency and dichroism of this band indicate that residues 39 and 46 are alpha-helical, with an axial orientation that is approximately 30 degrees relative to the membrane normal. Upon exposure to 2H2O (D2O), 30% of the peptide amide groups in hPLB undergo a slow deuterium/hydrogen exchange. The remainder of the protein, including the peptide groups of Leu-39 and Leu-42, appear inaccessible to exchange, indicating that most of the hPLB fragment is embedded in the lipid bilayer. By extending spectroscopic characterization of PLB to include hydrated, deuterated as well as site-directed isotope-labeled hPLB films, our results strongly support models of PLB that predict the existence of an alpha-helical hydrophobic region spanning the membrane domain.

Amino Acid Sequence↗

PubMed2003

Passive and iontophoretic transport enhancement of insulin through porcine epidermis by depilatories: permeability and fourier transform infrared spectroscopy studies.

The effect of thioglycolate-based depilatory lotions was studied on the in vitro passive and iontophoretic permeability of insulin through porcine epidermis and biophysical changes in the stratum corneum (SC) lipids and proteins. The porcine epidermis and Franz diffusion cells modified for iontophoresis were used for the in vitro transport studies. Cathodal iontophoresis was performed at 0.2 mA/cm2 current density. Resistance of the control- and depilatory-lotion-treated epidermis was determined according to Ohm's law. Biophysical changes were studied on porcine SC before (control) and after treatment with the depilatory lotions using Fourier transform infrared (FT-IR) spectroscopy. Asymmetric (approximately 2915 cm(-1)) and symmetric approximately 2848 cm(-1)) Carbon-Hydrogen (C-H) stretching absorbances were studied to estimate the extent of lipid extraction. Fourier self-deconvolution and second derivative procedures were applied to amide I band (1700-1600 cm(-1)) in order to estimate quantitatively the changes in the secondary structure of the SC protein. The passive permeability of insulin was significantly (P <.05) increased through depilatory-lotion-treated (ie, Better Off, Marzena, and Sally Hansen) epidermis in comparison to control. Iontophoresis significantly enhanced (P <.05) the permeability of insulin through depilatory-pretreated epidermis in comparison with the control epidermis. Further, we were able to achieve the desired flux of insulin (5.25 U/cm2/d) through Better Off-treated epidermis using 0.2 mA/cm2 current density and 100 U/mL donor concentration of insulin. The SC treated with depilatory lotions showed a decrease in peak areas of C-H stretching absorbances in comparison with untreated SC. Depilatory lotion treatment also decreased (P <.05) the epidermal resistance in comparison with the control epidermis. The decrease in the alpha-helix conformation and the increase in the random and turn structures were observed in the SC proteins due to depilatory lotion treatment. The changes in the secondary structure of proteins and lipid extraction from the SC are suggested as the cause of the decrease in the epidermal resistance and the increase in the passive and iontophoretic permeability of insulin through depilatory-pretreated epidermis in comparison with the control epidermis.

Animals↗

PubMed1993

Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman, and Fourier transform infrared spectroscopy.

There is considerable uncertainty about the precise secondary structure adopted by the M13 coat protein when embedded in a phospholipid bilayer. Circular dichroism (CD) spectroscopy suggests that a major change in the structure of the coat protein occurs upon membrane insertion. It is reported that the structure of the protein in the membrane has only about 50% alpha-helix, the rest being mainly in a beta-sheet conformation, whereas the protein is almost completely alpha-helical when intact in the phage. In this study we have undertaken a spectroscopic analysis using Fourier transform infrared, Raman, and CD spectroscopy to characterize the secondary structure of M13 coat protein when present in membranes consisting of dioleoylphosphatidylglycerol and dimyristoylphosphatidylglycerol. In sharp contrast to earlier CD studies, our results indicate that the coat protein in its membrane-embedded state has a very high alpha-helical content with virtually no beta-sheet structures present. This result indicates that the structures of the coat protein when intact in the phage or when embedded in the membrane are similar. Although our results differ from earlier CD studies, they are consistent with a recent NMR study, which showed that the M13 coat protein in sodium dodecyl sulfate micelles is primarily alpha-helical with no evidence for beta-sheet structure [Henry, G. D., & Sykes, B.D. (1992) Biochemistry 31, 5284-5297]. These results lead to the conclusion that the M13 coat protein can insert from the membrane-bound state into a virus particle with a similar secondary structure, without large energy implications.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophage M13↗

PubMed2005

Characterization of historic silk by polarized attenuated total reflectance Fourier transform infrared spectroscopy for informed conservation.

When assessing historic textiles and considering appropriate conservation, display, and storage strategies, characterizing the physical condition of the textiles is essential. Our work has concentrated on developing nondestructive or micro-destructive methodologies that will permit this. Previously, we have demonstrated a correlation between the physical deterioration of unweighted and "pink" tin (IV) chloride weighted silk and certain measurable spectroscopic and chromatographic signatures, derived from polarized Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy (Pol-ATR) and high-performance liquid chromatography (HPLC) microsampling analyses. The application of the Pol-ATR technique to aged silk characterization has now been extended to include a more comprehensive range of weighting methods and aging regimes. This was intended to replicate the full spectrum of states of deterioration observed in silk textiles, from pristine to heavily degraded. Breaking strength was employed as a measure of the physical integrity of the fibers, and, as expected, decreased with aging. An orientational crystallinity parameter, reflecting the microstructural ordering of the fibroin polymer within the fibers, was derived from the Pol-ATR spectra. A good correlation was observed between the breaking strength of the variety of fibers and this parameter. This suggests that the physical state of historic silk fabrics might be adequately characterized for conservation purposes by such indirect micromethodology.

Animals↗

PubMed1994

The secondary structure of the von Willebrand factor type A domain in factor B of human complement by Fourier transform infrared spectroscopy. Its occurrence in collagen types VI, VII, XII and XIV, the integrins and other proteins by averaged structure predictions.

The type A domain of the von Willebrand Factor is found also in the complement proteins factor B (FB), C2, CR3 and CR4, the integrins, collagen types VI, VII, XII and XIV, and other proteins. FB is a component of the alternative pathway of the complement system of immune defence, and is cleaved into the fragments Bb and Ba during complement activation. Bb contains a von Willebrand Factor type A (vWF) domain of unknown secondary structure and a serine proteinase (SP) domain, whereas Ba contains three short consensus repeat/complement control protein (SCR/CCP) domains. Fourier transform infrared (FT-IR) spectroscopy on a recombinant vWF domain and on FB and its Bb and Ba fragments shows a broad amide I band. In H2O buffer, second derivative spectra of the amide I band show subcomponents at 1654 to 1657 cm-1, which is typical of alpha-helix, and at 1676 to 1685 cm-1 and 1636 to 1637 cm-1, which are typical of beta-strand. alpha-Helix was detected in the vWF domain, the Bb fragment and FB, and the proportion of alpha-helix present decreased in that order. This shows that the vWF domain contains appreciable amounts of alpha-helix, while the SP and SCR/CCP domains are almost entirely beta-sheet in their secondary structures. Quantitative integration of the vWF FT-IR spectrum showed that this contained 31% alpha-helix and 36% beta-sheet. In 2H2O buffer, the alpha-helix content in the vWF domain is sensitive to the solvent, while the beta-sheet content is less so. An alignment of 75 vWF type A sequences from 25 proteins was used for averaged secondary structure predictions of the total length of 206 residues by the Robson and Chou-Fasman methods. In support of the FT-IR analysis, a total of at least five well-predicted alpha-helices (35% of residues) and at least five well-predicted beta-strands (21% of residues) were identified by both predictive methods, all of which were interspersed by regions of coil or turn conformations. Eight of the ten predicted alpha-helices and beta-strands form an alternating arrangement with each other. Since the predicted alpha-helices are mostly amphipathic, and since the alpha-helix FT-IR band is sensitive to solvent, the alpha-helices are inferred to be on the protein surface.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed2004

Probing the Q-proton pathway of ba3-cytochrome c oxidase by time-resolved Fourier transform infrared spectroscopy.

In cytochrome c oxidase, the terminal respiratory enzyme, electron transfers are strongly coupled to proton movements within the enzyme. Two proton pathways (K and D) containing water molecules and hydrophobic amino acids have been identified and suggested to be involved in the proton translocation from the mitochondrial matrix or the bacterial cytoplasm into the active site. In addition to the K and D proton pathways, a third proton pathway (Q) has been identified only in ba3-cytochrome c oxidase from Thermus thermophilus, and consists of residues that are highly conserved in all structurally known heme-copper oxidases. The Q pathway starts from the cytoplasmic side of the membrane and leads through the axial heme a3 ligand His-384 to the propionate of the heme a3 pyrrol ring A, and then via Asn-366 and Asp-372 to the water pool. We have applied FTIR and time-resolved step-scan Fourier transform infrared (TRS2-FTIR) spectroscopies to investigate the protonation/deprotonation events in the Q-proton pathway at ambient temperature. The photolysis of CO from heme a3 and its transient binding to CuB is dynamically linked to structural changes that can be tentatively attributed to ring A propionate of heme a3 (1695/1708 cm(-1)) and to deprotonation of Asp-372 (1726 cm(-1)). The implications of these results with respect to the role of the ring A propionate of heme a3-Asp372-H2O site as a proton carrier to the exit/output proton channel (H2O pool) that is conserved among all structurally known heme-copper oxidases, and is part of the Q-proton pathway in ba3-cytochrome c oxidase, are discussed.

Cell Membrane↗