Evaluation of the information content in infrared spectra for protein secondary structure determination

Regulation by CRAMP of the responses of murine peritoneal macrophages to extracellular ATP

Peritoneal macrophages were isolated from wild type (WT) mice and from mice invalidated for the P2X(7) receptor (KO) which had been pretreated with thioglycolate. In cells from WT mice, 1 mM ATP increased the intracellular concentration of calcium ([Ca(2+)](i)), the uptake of ethidium bromide, the production of reactive oxygen species (ROS), the secretion of IL-1beta, the release of oleic acid and of lactate dehydrogenase; it decreased the intracellular concentration of potassium ([K(+)](i)). In KO mice, ATP transiently increased the [Ca(2+)](i) confirming that the P2X(7) receptor is a major receptor of peritoneal macrophages. WKYMVm, an agonist of receptors for formylated peptides (FPR) also increased the [Ca(2+)](i) in murine macrophages. The slight increase of the [Ca(2+)](i) was strongly potentiated by ivermectin confirming the expression of functional P2X(4) receptors by murine peritoneal macrophages. CRAMP, the unique antimicrobial peptide derived from cathelin in mouse inhibited all the responses coupled to P2X(7) receptors in macrophages from WT mice. Agonists for FPR had no effect on the increase of the [Ca(2+)](i) in response to ATP. CRAMP had no effect on the increase of the [Ca(2+)](i) evoked by a combination of ATP and ivermectin in macrophages from P2X(7)-KO mice. In summary CRAMP inhibits the responses secondary to the activation of the murine P2X(7) receptors expressed by peritoneal macrophages. This inhibition is not mediated by FPR receptors and is specific since CRAMP has no effect on the response coupled to P2X(4) receptors. It can thus be concluded that the interaction between P2X(7) receptors and cathelin-derived antimicrobial peptides is species-specific, in some cases (man) positive in others (mouse) negative.

Quantitative and qualitative evaluation of adsorption/desorption of bovine serum albumin on hydrophilic and hydrophobic surfaces

We studied the adsorption of bovine serum albumin (BSA) from phosphate-buffered saline (pH 7.4) to hydrophilic and hydrophobic surfaces. Attenuated total reflection Fourier transform infrared spectroscopy, supported by spectral simulation, allowed us to determine with high precision the amount of BSA adsorbed (surface coverage) and its structural composition. The adsorbed BSA molecules had an alpha-helical structure on both hydrophobic and hydrophilic surfaces but had different molecular conformations and adsorption strengths on the two types of surface. Adsorption of BSA was saturated at around 50% surface coverage on the hydrophobic surface, whereas on the hydrophilic surface the adsorption reached 95%. The BSA molecules adsorbed to the hydrophilic surface with a higher interaction strength than to the hydrophobic surface. Very little adsorbed BSA could be desorbed from the hydrophilic surface, even using 0.1 M sodium dodecyl sulfate, a strong detergent solution. The formation of BSA-phosphate surface complexes was observed under different BSA adsorption conditions on hydrophobic and hydrophilic surfaces. The formation of these complexes correlated with the more efficient blocking of nonspecific interactions by the adsorbed BSA layer. Results from the molecular modeling of BSA interactions with hydrophobic and hydrophilic surfaces support the spectroscopic findings.

Collagen types analysis and differentiation by FTIR spectroscopy

Abnormal formation and organization of collagen network is commonly observed in many organ pathologies, but analytical techniques able to reveal the collagen biodistribution are still lacking. In this study, Fourier-transform infrared (FTIR) spectroscopy has been used to analyze type I, III, IV, V, and VI collagens, the most important compounds of connective tissues. A robust classification of 30 FTIR spectra per collagen type could be obtained by using a combination of four spectral intervals [nu(C=O) absorption of amide I (1,700-1,600 cm(-1)), delta(CH(2)), and delta(CH(3)) absorptions (1,480-1,350 cm(-1)), nu(C-N), and delta(N-H) absorptions of amide III (1,300-1,180 cm(-1)), and nu(C-O) and nu(C-O-C) absorptions of carbohydrate moieties (1,100-1,005 cm(-1))]. Then, a submolecular justification of this classification model was sought using a curve fitting analysis of the four spectral intervals. Results demonstrated that every spectral interval used for the classification contained highly discriminant absorption bands between all collagen types (multivariate analysis of variance, p < 0.01; Dunnett's T3 post hoc test, p < 0.05). All conditions seem thus joined to make FTIR spectroscopy and imaging major tools for implementing innovative methods in the field of molecular histology, which would be very helpful for the diagnosis of a wide range of pathologies.

Antiparallel beta-sheet: a signature structure of the oligomeric amyloid beta-peptide

AD (Alzheimer's disease) is linked to Abeta (amyloid beta-peptide) misfolding. Studies demonstrate that the level of soluble Abeta oligomeric forms correlates better with the progression of the disease than the level of fibrillar forms. Conformation-dependent antibodies have been developed to detect either Abeta oligomers or fibrils, suggesting that structural differences between these forms of Abeta exist. Using conditions which yield well-defined Abeta-(1-42) oligomers or fibrils, we studied the secondary structure of these species by ATR (attenuated total reflection)-FTIR (Fourier-transform infrared) spectroscopy. Whereas fibrillar Abeta was organized in a parallel beta-sheet conformation, oligomeric Abeta displayed distinct spectral features, which were attributed to an antiparallel beta-sheet structure. We also noted striking similarities between Abeta oligomers spectra and those of bacterial outer membrane porins. We discuss our results in terms of a possible organization of the antiparallel beta-sheets in Abeta oligomers, which may be related to reported effects of these highly toxic species in the amyloid pathogenesis associated with AD.

Protein secondary structure content in solution, films and tissues: redundancy and complementarity of the information content in circular dichroism, transmission and ATR FTIR spectra

The paper presents a simple and robust method to determine protein secondary structure from circular dichroism, transmission and attenuated total reflection (ATR) Fourier transform infrared spectra. It is found that the different spectroscopic methods bring valuable but roughly identical information on the secondary structure of proteins. ATR and transmission FTIR spectra display distinct differences, yet the secondary structure can be predicted from their spectra with roughly the same success. It is also found that one wavenumber or wavelength includes the large majority of the information correlated with secondary structure content and no more than 3 significant independent wavenumbers/wavelengths could be found for any of the spectroscopic data. This finding indicates that more complex linear combinations of the absorbance or ellipticities will not further improve secondary structure predictions. Furthermore, the information content in CD, transmission and ATR FTIR spectra is largely redundant. If combining CD and FTIR results in some improvement of structure prediction quality, the improvement is too modest to prompt spectroscopists to collect different spectroscopic data for structure prediction purposes. On the other hand, the data collected show that the quality of the FTIR spectrometers is such that biosensors or imaging methods sampling from 10(-9) to 10(-15) g yield spectra of sufficient quality to analyze protein secondary structure. These new techniques open the way to a new area of research, both in protein conformational response to ligand and imaging at sub-cellular scales.

Tertiary structure changes in albumin upon surface adsorption observed via fourier transform infrared spectroscopy

A nondestructive Fourier transform infrared (FTIR) spectroscopy assay, amenable to exploring a wide range of proteins and polymers, is used to measure changes in the tertiary structure of bovine serum albumin (BSA) adsorbed to three surfaces: gold, polystyrene (PS), and poly(D,L-lactic acid) (PDLLA). Tertiary structural analysis is important because typical secondary structural analysis (FTIR and CD) is not always sensitive enough to distinguish between the sometimes subtle protein structural changes caused by adsorption. The polymers are spin-coated onto a gold surface, exposed to protein, and then immersed in a deuterated buffer solution to probe the protein's tertiary structure before the sample is removed from its aqueous environment. Infrared band intensities, related to the exchange of amide hydrogen for deuterium (HDX), as a function of the immersion time in deuterated buffer, are used to determine the extent of amide solvent exposure. Analysis of the results in terms of a single exponential decay shows that enough amides undergo a measurable amount of exchange in 60 min to quantify relative changes in BSA solvent exposure on different surfaces. In addition, substantial fractions undergo HDX at a rate too fast or too slow to be followed with our experimental protocol. The proportions of these quickly and slowly exchanging amide groups also provide information about relative changes in the BSA structure on different surfaces. Adsorption was found to increase the extent of HDX over that observed for BSA in solution, consistent with surface-induced unfolding and a loss of tertiary structure. Changes in HDX were found to be more sensitive to which surface was absorbing the protein than the typical FTIR secondary structural analysis obtained from fitting the amide I band. HDX was greatest for BSA adsorbed to the surface of PDLLA and least in the case of BSA adsorbed to gold, which indicates the greatest and least degree of unfolding, respectively.

Ligand-receptor interactions in complex media: a new type of biosensors for the detection of coagulation factor VIII

Detection of receptor-ligand interaction in complex media remains a challenging issue. We report experimental results demonstrating the specific detection of the coagulation factor VIII in the presence of a large excess of other proteins using the new BIA-ATR technology based on attenuated total reflection Fourier transform infrared spectroscopy. The principle of the detection is related to the ability of factor VIII molecules to bind to lipid membranes containing at least 8% phosphatidylserine. Several therapeutic concentrates of factor VIII were analyzed and the binding of the coagulation factor was monitored as a function of time. We show that a non-specific adsorption of stabilizing agents (typically, von Willebrand factor and human serum albumin) may be avoided by controlling the geometry of the ATR element. A linear response of the sensors as a function of the factor VIII concentration is described for different lipid membrane compositions.

Characterization of dry globular proteins and protein fibrils by synchrotron radiation vacuum UV circular dichroism

Circular dichroism using synchrotron radiation (SRCD) can extend the spectral range down to approximately 130 nm for dry proteins, potentially providing new structural information. Using a selection of dried model proteins, including alpha-helical, beta-sheet, and mixed-structure proteins, we observe a low-wavelength band in the range 130-160 nm, whose intensity and peak position is sensitive to the secondary structure of the protein and may also reflect changes in super-secondary structure. This band has previously been observed for peptides but not for globular proteins, and is compatible with previously published theoretical calculations related to pi-orbital transitions. We also show that drying does not lead to large changes in the secondary structure and does not induce orientational artifacts. In combination with principal component analysis, our SRCD data allow us to distinguish between two different types of protein fibrils, highlighting that bona fide fibrils formed by lysozyme are structurally more similar to the nonclassical fibrillar aggregates formed by the SerADan peptide than with the amyloid formed by alpha-synuclein. Thus, despite the lack of direct structural conclusions, a comprehensive SRCD-based database of dried protein spectra may provide a useful method to differentiate between various types of supersecondary structure and aggregated protein species.

Expression, purification, and structural characterization of CfrA, a putative iron transporter from Campylobacter jejuni

The gene for the Campylobacter ferric receptor (CfrA), a putative iron-siderophore transporter in the enteric food-borne pathogen Campylobacter jejuni, was cloned, and the membrane protein was expressed in Escherichia coli, affinity purified, and then reconstituted into model lipid membranes. Fourier transform infrared spectra recorded from the membrane-reconstituted CfrA are similar to spectra that have been recorded from other iron-siderophore transporters and are highly characteristic of a beta-sheet protein (approximately 44% beta-sheet and approximately 10% alpha-helix). CfrA undergoes relatively extensive peptide hydrogen-deuterium exchange upon exposure to (2)H(2)O and yet is resistant to thermal denaturation at temperatures up to 95 degrees C. The secondary structure, relatively high aqueous solvent exposure, and high thermal stability are all consistent with a transmembrane beta-barrel structure containing a plug domain. Sequence alignments indicate that CfrA contains many of the structural motifs conserved in other iron-siderophore transporters, including the Ton box, PGV, IRG, RP, and LIDG motifs of the plug domain. Surprisingly, a homology model reveals that regions of CfrA that are expected to play a role in enterobactin binding exhibit sequences that differ substantially from the sequences of the corresponding regions that play an essential role in binding/transport by the E. coli enterobactin transporter, FepA. The sequence variations suggest that there are differences in the mechanisms used by CfrA and FepA to interact with bacterial siderophores. It may be possible to exploit these structural differences to develop CfrA-specific therapeutics.

FTIR Microspectroscopy Coupled with Two-Class Discrimination Segregates Markers Responsible for Inter- and Intra-Category Variance in Exfoliative Cervical Cytology

Infrared (IR) absorbance of cellular biomolecules generates a vibrational spectrum, which can be exploited as a “biochemical fingerprint” of a particular cell type. Biomolecules absorb in the mid-IR (2–20 μm) and Fourier-transform infrared (FTIR) microspectroscopy applied to discriminate different cell types (exfoliative cervical cytology collected into buffered fixative solution) was evaluated. This consisted of cervical cytology free of atypia (i.e. normal; n = 60), specimens categorised as containing low-grade changes (i.e. CIN1 or LSIL; n = 60) and a further cohort designated as high-grade (CIN2/3 or HSIL; n = 60). IR spectral analysis was coupled with principal component analysis (PCA), with or without subsequent linear discriminant analysis (LDA), to determine if normal versus low-grade versus high-grade exfoliative cytology could be segregated. With increasing severity of atypia, decreases in absorbance intensity were observable throughout the 1,500 cm⁻¹ to 1,100 cm⁻¹ spectral region; this included proteins (1,460 cm⁻¹), glycoproteins (1,380 cm⁻¹), amide III (1,260 cm⁻¹), asymmetric (ν_as) PO₂⁻ (1,225 cm⁻¹) and carbohydrates (1,155 cm⁻¹). In contrast, symmetric (ν_s) PO₂⁻ (1,080 cm⁻¹) appeared to have an elevated intensity in high-grade cytology. Inter-category variance was associated with protein and DNA conformational changes whereas glycogen status strongly influenced intra-category. Multivariate data reduction of IR spectra using PCA with LDA maximises inter-category variance whilst reducing the influence of intra-class variation towards an objective approach to class cervical cytology based on a biochemical profile.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

Amphetamine effects on brain protein structure and oxidative stress as revealed by FTIR microspectroscopy

Amphetamines are psychostimulants abused by man, that eventually leads to drug dependence. Amphetamine administration to rodents has been shown to provoke significant neurotoxicity involving dopaminergic nerve terminal degeneration. However, little information related to the effect of amphetamines on reactive oxygen species (ROS) production and neurotoxicity in brain is currently available. Herein we report the biochemical alterations of lipids and proteins in brain sections from amphetamine-treated rodents using infrared microspectroscopy, immunohistochemistry, and immunoblotting. The spectroscopic changes reveal for the first time the formation of beta-sheet-rich proteins in the cortex, but no significant protein alterations are visible in hippocampus region where hydroperoxide concentration is found to be lower relative to cortex. These result suggest that ROS generated by amphetamine-mediated oxidative stress induce formation beta-sheet-rich proteins which can be of amyloid beta-like character.

Structure of membrane-embedded M13 major coat protein is insensitive to hydrophobic stress

The structure of a membrane-embedded alpha-helical reference protein, the M13 major coat protein, is characterized under different conditions of hydrophobic mismatch using fluorescence resonance energy transfer in combination with high-throughput mutagenesis. We show that the structure is similar in both thin (14:1) and thick (20:1) phospholipid bilayers, indicating that the protein does not undergo large structural rearrangements in response to conditions of hydrophobic mismatch. We introduce a "helical fingerprint" analysis, showing that amino acid residues 1-9 are unstructured in both phospholipid bilayers. Our findings indicate the presence of pi-helical domains in the transmembrane segment of the protein; however, no evidence is found for a structural adaptation to the degree of hydrophobic mismatch. In light of current literature, and based on our data, we conclude that aggregation (at high protein concentration) and adjustment of the tilt angle and the lipid structure are the dominant responses to conditions of hydrophobic mismatch.

Infrared spectroscopy study on the conformational changes leading to pore formation of the toxin sticholysin II

The structure of the actinoporin sticholysin II (StnII) in the pore state was investigated by Fourier transform infrared spectroscopy in the attenuated total reflection configuration. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/cholesterol unilamellar vesicles were employed. The alpha-helix content increases in approximately 30% upon lipid binding, which agrees with an extension of eight or nine residues at the N-terminal helix. Furthermore, analyses of dichroic spectra show that the extended N-terminal helix would have a 31 degrees tilt with respect to the membrane normal. The orientation of the central beta-sandwich was also estimated. In addition, it was detected that StnII alters the orientation of the lipid acyl chains. (1)H/(2)H exchange experiments sustain a mainly superficial interaction between StnII and the membrane, with no protection of the beta-sandwich. The implications of the results in the mechanism of pore formation are discussed.

The integrin binding site 2 (IBS2) in the talin rod domain is essential for linking integrin beta subunits to the cytoskeleton

Talin1 is a large cytoskeletal protein that links integrins to actin filaments through two distinct integrin binding sites, one present in the talin head domain (IBS1) necessary for integrin activation and a second (IBS2) that we have previously mapped to talin residues 1984-2113 (fragment J) of the talin rod domain (1 Tremuth, L., Kreis, S., Melchior, C., Hoebeke, J., Ronde, P., Plancon, S., Takeda, K., and Kieffer, N. (2004) J. Biol. Chem. 279, 22258-22266), but whose functional role is still elusive. Using a bioinformatics and cell biology approach, we have determined the minimal structure of IBS2 and show that this integrin binding site corresponds to 23 residues located in alpha helix 50 of the talin rod domain (residues 2077-2099). Alanine mutation of 2 highly conserved residues (L2094A/I2095A) within this alpha helix, which disrupted the alpha-helical structure of IBS2 as demonstrated by infrared spectroscopy and limited trypsin proteolysis, was sufficient to prevent in vivo talin fragment J targeting to alphaIIbbeta3 integrin in focal adhesions and to inhibit in vitro this association as shown by an alphaIIbbeta3 pulldown assay. Moreover, expression of a full-length mouse green fluorescent protein-talin LI/AA mutant in mouse talin1(-/-) cells was unable to rescue the inability of these cells to assemble focal adhesions (in contrast to green fluorescent protein-talin wild type) despite the presence of IBS1. Our data provide the first direct evidence that IBS2 in the talin rod is essential to link integrins to the cytoskeleton.

Biochemical interaction analysis on ATR devices: a wet chemistry approach for surface functionalization

A new generic device suitable for the investigation of ligand-receptor interactions is presented. In particular, the research focused on optical waveguides constituted by an attenuated total internal reflection (ATR) element, transparent in the infrared and whose surfaces were activated in view of covalently binding a receptor. Silicon and germanium ATR elements were considered. The original method is based on the grafting of bifunctional spacer molecules directly at the surface of the germanium crystal, avoiding the deposition of an intermediate metal layer. The grafting of these binding molecules (under their N-hydroxysuccinimidyl ester forms) was performed either by wet chemistry or by photochemistry. The functionalized surfaces, which allow the binding of molecules bearing peripherical NH2 groups, were successfully used, e.g., for the detection of proteins (streptavidin) or of small molecules (biotin). In the latter case, the biotin was readily detected for concentrations as low as 10(-12) M.

Analysis of type I and IV collagens by FT-IR spectroscopy and imaging for a molecular investigation of skeletal muscle connective tissue

Many muscular diseases result from abnormal organization of connective tissue and/or collagen network formation. Only a few molecular imaging techniques are able to analyze this collagen network by differentiating collagen types. In this study, FT-IR spectroscopy was used to analyze type I and IV collagens, the most important compounds of which are perimysium and endomysium, respectively. Secondary structure of collagen types was determined by curve-fitting the 1,700-1,480 cm(-1) spectral interval. Type I collagen could be differentiated from type IV by its higher amounts of triple helix and alpha-helix, but lower amounts of beta-sheets (P < 0.01). FT-IR imaging was then used to determine structural features of perimysium and endomysium collagen network in bovine Flexor carpi radialis muscle. Secondary structure of proteins contained in perimysium and endomysium was found to be very close to type I and IV collagens, respectively. FT-IR spectroscopy and imaging are thus analytical tools that might be used for investigating biodistribution and assembly of collagen types in connective tissues.

Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra

A model for the calculation of amide I FTIR and 2DIR spectra taking into account fluctuations in hydrogen bonding and structure from molecular dynamics (MD) simulations is tested on three systems. It is found that although the homogeneous lineshape approximation yields satisfactory FTIR spectra, 2DIR spectra are sensitive to the inhomogeneity naturally present in any solvated protein and the common approximations of a static structure and averaged-effect solvent are invalid. By building on the local amide Hamiltonian and incorporating site energy variation with electrostatic-based models and disorder from MD trajectories, good agreement is obtained between calculated and measured 2DIR spectra. The largest contribution to the observed inhomogeneity is found to be the fluctuating site energies, which in turn are most sensitive to the water solvent. With the ability to accurately predict 2DIR spectra from atomistic simulations, new opportunities to test force fields and mechanistic predictions from MD are revealed.