Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy

Deciphering Cadmium (Cd) Tolerance in Newly Isolated Bacterial Strain, Ochrobactrum intermedium BB12, and Its Role in Alleviation of Cd Stress in Spinach Plant (Spinacia oleracea L.)

A cadmium (Cd)-tolerant bacterium Ochrobactrum intermedium BB12 was isolated from sewage waste collected from the municipal sewage dumping site of Bhopal, India. The bacterium showed multiple heavy metal tolerance ability and had the highest minimum inhibitory concentration of 150 mg L-1 of Cd. Growth kinetics, biosorption, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy studies on BB12 in the presence of Cd suggested biosorption as primary mode of interaction. SEM and TEM studies revealed surface deposition of Cd. FTIR spectra indicated nitrogen atom in exopolysaccharides secreted by BB12 to be the main site for Cd attachment. The potential of BB12 to alleviate the impact of Cd toxicity in spinach plants (Spinacia oleracea L.) var. F1-MULAYAM grown in the soil containing Cd at 25, 50, and 75 mg kg-1 was evaluated. Without bacterial inoculation, plants showed delayed germination, decrease in the chlorophyll content, and stunted growth at 50 and 75 mg kg-1 Cd content. Bacterial inoculation, however, resulted in the early germination, increased chlorophyll, and increase in shoot (28.33%) and root fresh weight (72.60%) at 50 mg kg-1 of Cd concentration after 75 days of sowing. Due to bacterial inoculation, elevated proline accumulation and lowered down superoxide dismutase (SOD) enzyme activity was observed in the Cd-stressed plants. The isolate BB12 was capable of alleviating Cd from the soil by biosorption as evident from significant reduction in the uptake/translocation and bioaccumulation of Cd in bacteria itself and in the plant parts of treated spinach. Potential PGP prospects and heavy metal bioremediation capability of BB12 can make the environmental application of the organism a promising approach to reduce Cd toxicity in the crops grown in metal-contaminated soils.

Infrared spectroscopy with multivariate analysis to interrogate the interaction of whole cells and secreted soluble exopolimeric substances of Pseudomonas veronii 2E with Cd(II), Cu(II) and Zn(II)

Extracellular polymeric substances (EPS) are bacterial products associated to cell wall or secreted to the liquid media that form the framework of microbial mats. These EPS contain functional groups as carboxyl, amino, hydroxyl, phosphate and sulfhydryl, able to interact with cations. Thus, EPS may be considered natural detoxifying compounds of metal polluted waters and wastewaters. In this work Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR) in combination with multivariate analysis (Principal Component Analysis-PCA-) were used to study the interaction of Cd(II), Cu(II) and Zn(II) and Pseudomonas veronii 2E cells, including bound EPS and cell wall, and its different soluble EPS fractions, previously characterized as Cd(II) ligands of moderate strength. Amino groups present in exopolysaccharide fraction were responsible for Zn(II) and Cu(II) complexation, while carboxylates chelated Cd(II). In lipopolysaccharide fraction, phosphoryl and carboxyl sites were involved in Cd(II) and Cu(II) binding, while Zn(II) interacted with amino groups. Similar results were obtained from cells. These studies confirmed that FTIR-PCA is a rapid analytical tool to provide valuable information regarding the functional groups in biomolecules related to metal interaction. Moreover, a discrimination and identification of functional groups present in both EPS and cells that interacted with Cd(II), Zn(II) and Cu(II) was demonstrated.

Plant Response to Engineered Metal Oxide Nanoparticles

All metal oxide nanoparticles influence the growth and development of plants. They generally enhance or reduce seed germination, shoot/root growth, biomass production and physiological and biochemical activities. Some plant species have not shown any physiological change, although significant variations in antioxidant enzyme activity and upregulation of heat shock protein have been observed. Plants have evolved antioxidant defence mechanism which involves enzymatic as well as non-enzymatic components to prevent oxidative damage and enhance plant resistance to metal oxide toxicity. The exact mechanism of plant defence against the toxicity of nanomaterials has not been fully explored. The absorption and translocation of metal oxide nanoparticles in different parts of the plant depend on their bioavailability, concentration, solubility and exposure time. Further, these nanoparticles may reach other organisms, animals and humans through food chain which may alter the entire biodiversity. This review attempts to summarize the plant response to a number of metal oxide nanoparticles and their translocation/distribution in root/shoot. The toxicity of metal oxide nanoparticles has also been considered to see if they affect the production of seeds, fruits and the plant biomass as a whole.

Differential effects of cerium oxide nanoparticles on rice, wheat, and barley roots: a fourier transform infrared (FT-IR) microspectroscopy study

Cerium oxide nanoparticles (nCeO2) have extensive industrial applications, and concerns regarding their threat to the environment have been raised. This study includes structural analysis of intact root xylem of rice (Oryza sativaL.), wheat (Triticum aestivumL.), and barley (Hordeum vulgareL.) seedlings exposed to nCeO2 suspensions (0, 62.5, 125, 250, and 500 mg L(-1)). Fourier transform infrared microspectroscopy was applied to determine compositional alterations in the root xylem, and principal component analysis (PCA) was carried out to examine spectral differences between nCeO2 treatments. Results demonstrated that nCeO2 at ≥ 125 mg L(-1) changed the region of spectra around 1696-1760 cm(-1) in rice root, 125 and 250 mg L(-1) modified 1744-1792 cm(-1) in wheat, and 62.5 and 125 mg L(-1) altered 1727-1760 cm(-1) in barley. PCA afforded the clustering of nCeO2 treatments at 0 and 62.5 mg L(-1) in rice and wheat and 0 and 500 mg L(-1) in barley. Furthermore, major peaks at 1744 or 1760 cm(-1) appeared in primary PC and 1728 cm(-1) in secondary PC score loadings. These findings illustrated that nCeO2 induced compositional modifications in the root xylem of cereals.

Thermogravimetric and decomposition kinetic studies of Mesua ferrea L. deoiled cake

The present study aims to explore the physico-chemical properties of Mesua ferrea L. (Iron wood tree) deoiled cake (MFDC) and decomposition parameters for thermochemical methods of conversion. The physico-chemical characteristics of MFDC were investigated by bomb calorimetry, TG/DTA (10, 20 and 40°C min(-1)), elemental analysis (CHN) and FTIR spectroscopy. The proximate composition was calculated using standard ASTM methodology. The temperature profile, activation energy (E), pre-exponential factor (A) and reaction order (n) for the active pyrolysis zone of the species under investigation have been provided for the respective heating rates using Arrhenius, Coats-Redfern, Flynn-Wall-Ozawa (FWO) and Global independent reactions model. The current investigation suggests that within the realm of existing biomass conversion technologies, MFDC can be used as a feedstock for thermochemical conversion.

Use of Fourier Transform Infrared (FTIR) Spectroscopy to Study Cadmium-Induced Changes in Padina Tetrastromatica (Hauck)

The aim of this study is to adopt the approach of metabolic fingerprinting through the use of Fourier Transform Infrared (FTIR) technique to understand changes in the chemical structure in Padina tetrastromatica (Hauck). The marine brown alga under study was grown in two different environmental conditions; in natural seawater ( P. tetrastromatica (c)) and in seawater suplemented with 50 ppm of cadmium ( P. tetrastromatica (t)) for a three-week period in the laboratory. The second derivative, IR specrum in the mid-infrared region (4000-400 cm-1) was used for discriminating and identifying various functional groups present in P. tetrastromatica (c). On exposure to Cd, P. tetrastromatica (t) accumulated 412 ppm of Cd and showed perturbation in the band structure in the mid-IR absorption region. Variation in spectral features of the IR bands of P. tetrastromatica (untreated and treated) suggests that cadmium ions bind to hydroxyl, amino, carbonyl and phosphoryl functionalities. This was attributable to the presence of the following specific bands. A band at 3666 cm-1 in untreated P. tetrastromatica (c) while a band at 3560 cm-1 in Cd-treated P. tetrastromatica (t) due to non bonded and bonded O-H respectively. Similarly, non bonded N-H for P. tetrastromatica (c) showed two bands at 3500 cm-1 and 3450 cm-1 due to the N-H stretching vibrations and a band at 1577cm-1 due to N-H bending vibrations, while an intense band at 3350 cm-1 due to bonded N-H stretching vibrations and at 1571 cm-1 due to bending vibrations was observed for Cd-treated P. tetrastromatica (t). Involvement of ester carbonyl group is characterized by the presence of a band at 1764 cm-1 in untreated P. tetrastromatica (c) while the Cd-treated P. tetrastromatica (t) showed the band at 1760 cm-1. The intensity of the band at 1710 cm-1 in the control samples decreased drastically after cadmium treatment indicating carbonyl of COOH to be involved in metal chelation. A band at 1224 cm-1 for untreated P. tetrastromatica ( c) and at 1220 cm-1 for Cd-treated P. tetrastromatica (t) is indicative of the involvement of phosphoryl group in metal binding. Several other such changes were also evident and discussed in this paper. Based on our observation, FTIR technique proves to be an efficient tool for detecting structural changes and probable binding sites induced by the presence of a metal pollutant, cadmium, in the marine environment.

Structural differences between TSEs strains investigated by FT-IR spectroscopy

Strain diversity in transmissible spongiform encephalopathies (TSEs) has been suggested to be "enciphered" in the structure of the misfolded prion protein isoform PrP(Sc). We have recently demonstrated the strain typing potential of the FT-IR spectroscopy technique, analyzing four different TSE agents adapted to Syrian hamsters [A. Thomzig, S. Spassov, M. Friedrich, D. Naumann and M. Beekes, Discriminating scrapie and BSE isolates by infrared spectroscopy of pathological prion protein J. Biol. Chem. 279 (2004) 33847-33854.] [1]. In the present paper, we have extended the FT-IR study, exploring the secondary structure, temperature stability, and hydrogen-deuterium exchange characteristics of PrP27-30, from the TSE agents 263K, ME7-H, 22A-H, and BSE-H. The strain differentiation capacity of the FT-IR approach was objectively proven for the first time by multivariate cluster analysis. The second derivative FT-IR spectra obtained from dried protein films or samples hydrated in H(2)O or D(2)O consistently exhibited strain-specific infrared characteristics in the secondary structure sensitive amide I region, complemented by strain dependent spectral traits in the amide II and amide A absorption regions, and the different H/D-exchange behaviour of the various PrP27-30 samples. FT-IR spectra of PrP27-30 samples from 263K, ME7-H and 22A-H exposed to increasing temperature (up to 90 degrees C) showed that a strain-specific response to heat treatment is associated with strain specific thermostability of distinct secondary structure elements, providing additional means for TSEs strain discrimination.

Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy

Water from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance (ATR) accessory. However, when protein solutions are studied, ATR spectroscopy suffers from several drawbacks, the most severe being nonproportionality of the observed absorbance with the protein concentration and spectral distortions that vary from protein to protein and from sample to sample. In this study, we show (1) that the nonproportionality is due to adsorption of the protein on the ATR crystal surface; (2) that the contribution of the crystal-adsorbed protein can easily be taken into account, rendering the corrected absorbance proportional to the protein concentration; (3) that the observed variable base line distortions, likely due to changes in the penetration depth of the light beam in solutions with the refractive index that depends on the protein concentration, can be easily eliminated; and (4) that ATR IR spectra thus corrected for protein adsorption and light penetration can be used to properly analyze the secondary structure of proteins in solution.

Maximum entropy deconvolution of infrared spectra: use of a novel entropy expression without sign restriction

Absorbance and difference infrared spectra are often acquired aiming to characterize protein structure and structural changes of proteins upon ligand binding, as well as for many other chemical and biochemical studies. Their analysis requires as a first step the identification of the component bands (number, position, and area) and as a second step their assignment. The first step of the analysis is challenged by the habitually strong band overlap in infrared spectra. Therefore, it is useful to make use of a mathematical method able to narrow the component bands to the extent to eliminate, or at least reduce, the band overlap. Additionally, to be of general applicability this method should permit negative values for the solution. We present a maximum entropy deconvolution approach for the band-narrowing of absorbance and difference spectra showing the required characteristics, which uses the generalized negative Burg-entropy (Itakura-Saito discrepancy) generalized for difference spectra. We present results on synthetic noisy absorbance and difference spectra, as well as on experimental infrared spectra from the membrane protein bacteriorhodopsin.

Protein conformations, interactions, and H/D exchange

Modern mass spectrometry (MS) is well known for its exquisite sensitivity in probing the covalent structure of macromolecules, and for that reason, it has become the major tool used to identify individual proteins in proteomics studies. This use of MS is now widespread and routine. In addition to this application of MS, a handful of laboratories are developing and using a methodology by which MS can be used to probe protein conformation and dynamics. This application involves using MS to analyze amide hydrogen/deuterium (H/D) content from exchange experiments. Introduced by Linderstøm-Lang in the 1950s, H/D exchange involves using (2)H labeling to probe the rate at which protein backbone amide protons undergo chemical exchange with the protons of water. With the advent of highly sensitive electrospray ionization (ESI)-MS, a powerful new technique for measuring H/D exchange in proteins at unprecedented sensitivity levels also became available. Although it is still not routine, over the past decade the methodology has been developed and successfully applied to study various proteins and it has contributed to an understanding of the functional dynamics of those proteins.

Changes in protein conformation and dynamics upon complex formation of brain-derived neurotrophic factor and its receptor: investigation by isotope-edited Fourier transform IR spectroscopy

The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly beta strands (approximately 53%) and relatively low contents of other secondary structures including beta turns (approximately 16%), disordered structures (approximately 12%), and loops (approximately 18%) and is deficient in alpha helix. We also observe that trkB in solution contains mostly beta strands (52%) and little alpha helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly beta turns and disordered structures while the majority of the beta-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to beta strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H-D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand-receptor complex that is in contrast to other ligand-receptor complexes such as a cytokine-receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation.

Thermal unfolding of ribonuclease A in phosphate at neutral pH: deviations from the two-state model

The thermal denaturation of ribonuclease A (RNase A) in the presence of phosphate at neutral pH was studied by differential scanning calorimetry (DSC) and a combination of optical spectroscopic techniques to probe the existence of intermediate states. Fourier transform infrared (FTIR) spectra of the amide I' band and far-uv circular dichroism (CD) spectra were used to monitor changes in the secondary structure. Changes in the tertiary structure were monitored by near-uv CD. Spectral bandshape changes with change in temperature were analyzed using factor analysis. The global unfolding curves obtained from DSC confirmed that structural changes occur in the molecule before the main thermal denaturation transition. The analysis of the far-uv CD and FTIR spectra showed that these lower temperature-induced modifications occur in the secondary structure. No pretransition changes in the tertiary structure (near-uv CD) were observed. The initial changes observed in far-uv CD were attributed to the fraying of the helical segments, which would explain the loss of spectral intensity with almost no modification of spectral bandshape. Separate analyses of different regions of the FTIR amide I' band indicate that, in addition to alpha-helix, part of the pretransitional change also occurs in the beta-strands.

Pressure versus temperature unfolding of ribonuclease A: an FTIR spectroscopic characterization of 10 variants at the carboxy-terminal site

FTIR spectroscopy was used to characterize and compare the temperature- and pressure-induced unfolding of ribonuclease A and a set of its variants engineered in a hydrophobic region of the C-terminal part of the molecule postulated as a CFIS. The results show for all the ribonucleases investigated, a cooperative, two-state, reversible unfolding transition using both pressure and temperature. The relative stabilities, among the different sites and different variants at the same site, monitored either through the changes in the position of the maximum of the amide I' band and the tyrosine band, or the maximum of the band assigned to the beta-sheet structure, corroborate the results of a previous study using fourth-derivative UV absorbance spectroscopy. In addition, variants at position 108 are the most critical for ribonuclease structure and stability. The V108G variant seems to present a greater conformational flexibility than the other variants. The pressure- and temperature-denaturated states of all the ribonucleases characterized retained some secondary structure. However, their spectral maxima were centered at different wavenumbers, which suggests that pressure- and temperature-denaturated states do not have the same structural characteristics. Nevertheless, there was close correlation between the pressure and temperature midpoint transition values for the whole series of protein variants, which indicated a common tendency of stability toward pressure and heat.

Hydrogen peroxide-induced structural alterations of RNAse A

Proteins exposed to oxidative stress are degraded via proteolytic pathways. In the present study, we undertook a series of in vitro experiments to establish a correlation between the structural changes induced by mild oxidation of the model protein RNase A and the proteolytic rate found upon exposure of the modified protein toward the isolated 20 S proteasome. Fourier transform infrared spectroscopy was used as a structure-sensitive probe. We report here strong experimental evidence for oxidation-induced conformational rearrangements of the model protein RNase A and, at the same time, for covalent modifications of amino acid side chains. Oxidation-related conformational changes, induced by H(2)O(2) exposure of the protein may be monitored in the amide I region, which is sensitive to changes in protein secondary structure. A comparison of the time- and H(2)O(2) concentration-dependent changes in the amide I region demonstrates a high degree of similarity to spectral alterations typical for temperature-induced unfolding of RNase A. In addition, spectral parameters of amino acid side chain marker bands (Tyr, Asp) revealed evidence for covalent modifications. Proteasome digestion measurements on oxidized RNase A revealed a specific time and H(2)O(2) concentration dependence; at low initial concentration of the oxidant, the RNase A turnover rate increases with incubation time and concentration. Based on these experimental findings, a correlation between structural alterations detected upon RNase A oxidation and proteolytic rates of RNase A is established, and possible mechanisms of the proteasome recognition process of oxidatively damaged proteins are discussed.

Proteolytic degradation of ribonuclease A in the pretransition region of thermally and urea-induced unfolding

The method of limited proteolysis has proven to be appropriate for the determination of unfolding rate constants (k(U)) of ribonuclease A in the transition region of thermal denaturation [Arnold, U. & Ulbrich-Hofmann, R. (1997) Biochemistry 36, 2166-2172]. The aim of the present paper was to extend this procedure to the pretransition region of thermally and urea-induced denaturation where spectroscopic methods do not allow direct measurement of k(U). The results show that the approach can be applied successfully to denaturing (free energy of unfolding Delta G < 10 kJ.mol(-1)) and to marginally native conditions (Delta G = 10-25 kJ.mol(-1)). Under moderately (Delta G = 25-30 kJ.mol(-1)) and strongly native conditions (Delta G > 30 kJ.mol(-1)), however, the determination of kU was not possible in this way as the proteolytic degradation of ribonuclease A by thermolysin or trypsin was no longer determined by global unfolding. Here, proteolysis proceeds via the native RNase A. In the presence of low concentrations of urea, the rate constants of proteolysis were, surprisingly, smaller than in the absence of urea. As the protease activity has been taken into account, this result points to a local stabilization of the RNase A molecule.

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.

Conformational properties of the A-state of cytochrome c studied by hydrogen/deuterium exchange and electrospray mass spectrometry

Hydrogen/deuterium (H/D) exchange studies that were monitored by liquid chromatography-electrospray ionization mass spectrometry (LC-ESIMS) were used to obtain a structural description of the compact acid-denatured state of ferricytochrome c (A-state). Due to the very different solvent conditions necessary to generate the nonnative states, it was essential that after deuterium labeling the nonnative states were refolded to the native state to insure high reproducibility during sample preparation and LC-ESIMS analysis. Approximately 30% lower deuterium was found incorporated in the A-state compared to the acid-denatured (UA) state. The analysis of the width of the mass peak suggests that the distribution of conformers sampled in the A-state was relatively narrow and that the compactness of the A-state was much closer to that of the native state than to the acid-denatured state. The LC-ESIMS study of partially deuterium-labeled peptic fragments derived from the A-state conformer generated under H/D quenching conditions were interpreted in terms of a significant loss of structural integrity within amino acid region 22-46.