On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy

Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.     

ATR and transmission analysis of pigments by means of far infrared spectroscopy

In the field of FTIR spectroscopy, the far infrared (FIR) spectral region has been so far less investigated than the mid-infrared (MIR), even though it presents great advantages in the characterization of those inorganic compounds, which are inactive in the MIR, such as some art pigments, corrosion products, etc. Furthermore, FIR spectroscopy is complementary to Raman spectroscopy if the fluorescence effects caused by the latter analytical technique are considered. In this paper, ATR in the FIR region is proposed as an alternative method to transmission for the analyses of pigments. This methodology was selected in order to reduce the sample amount needed for analysis, which is a must when examining cultural heritage materials. A selection of pigments have been analyzed in both ATR and transmission mode, and the resulting spectra were compared with each other. To better perform this comparison, an evaluation of the possible effect induced by the thermal treatment needed for the preparation of the polyethylene pellets on the transmission spectra of the samples has been carried out. Therefore, pigments have been analyzed in ATR mode before and after heating them at the same temperature employed for the polyethylene pellet preparation. The results showed that while the heating treatment causes only small changes in the intensity of some bands, the ATR spectra were characterized by differences in both intensity and band shifts towards lower frequencies if compared with those recorded in transmission mode. All pigments' transmission and ATR spectra are presented and discussed, and the ATR method was validated on a real case study. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular modeling and spectroscopic studies on binding of 2,6-bis[4-(4-amino-2-trifluoromethylphenoxy)benzoyl] pyridine to human serum albumin

BAFP (2,6-bis[4-(4-amino-2-trifluoromethylphenoxy)benzoyl] pyridine), a synthesized polyimide compound, was exploited for the first time to analyze its interaction with human serum albumin (HSA) by molecular modeling, fluorescence and Fourier transform infrared attenuated total reflection spectroscopy (FTIR ATR) with drug concentrations of 3.3 × 10⁻⁶ to 3.0 × 10⁻⁵ mol L⁻¹. Molecular docking was performed to reveal the possible binding mode. The results suggested that BAFP can strongly bind to human serum albumin (HSA) and the primary binding site of BAFP is located in site II of HSA, which is supported by the results from the competitive experiment. The binding constants for the interaction of BAFP with HSA have been evaluated from relevant fluorescence data at different temperatures (296, 303, 310 and 308 K). The alterations of the protein secondary structure in the presence of BAFP in aqueous solution were quantitatively calculated by the evidences from FTIR ATR spectroscopes. The binding process was exothermic and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction, which is also in good agreement with the results of molecule modeling study. The enthalpy change ΔH⁰, the free energy change ΔG⁰ and the entropy change ΔS⁰ of 296 K were calculated to be −7.75, −27.68 kJ mol⁻¹ and 67.33 J mol⁻¹ K⁻¹, respectively.     

Finite-Difference Time-Domain Analysis of the Interaction of Gaussian Evanescent Light with a Single Dielectric Sphere or Ordered Dielectric Spheres

The interaction of gaussian evanescent light with a single dielectric sphere or ordered dielectric spheres in an attenuated total reflection (ATR) geometry was analyzed by the finite-difference time-domain method. Various aspects of this interaction were investigated in terms of spatial visualizations of light intensity, reflectance vs. wavelength characteristics, the transient behavior of reflectances, and so forth. In the case of a single sphere, it was evident that the whispering gallery mode can be excited in ATR geometries, but such excitation cannot be easily confirmed only through the observation of wavelength-scanned ATR spectra. In the case of a closely packed two-dimensional array of dielectric spheres, it was found that an easy axis and also a difficult axis for light propagation exist.This paper was originally presented at the 5th International Conference on NEAR FIELD OPTICS and RELATED TECHNOLOGIES (NFO-5), which was held on December 6–10, 1998 at Coganoi Bay Hotel, Shirahama, Japan, in cooperation with the Japan Society of Applied Phisics and Mombusho Grantin Aid for Scientific Research on Priority Areas “Near-field Nano-optics” Project, sponsored by Japan Society for the Promotion of Science.     

Synchronous ATR infrared and NIR-spectroscopy investigation of sepiolite upon drying

A new environmental cell allowing for the independent synchronous collection of the near- and mid-infrared spectra (12,000–600 cm⁻¹) in the diffuse reflection and attenuated total reflection (ATR) modes, respectively, is reported. The cell is employed to study in real time the dehydration of the phyllosilicate mineral sepiolite, Mg₈Si₁₂O₃₀(OH)₄(OH₂)₄·wH₂O, in both its natural form and after in situ deuteration at ambient. The spectra are obtained under dynamic purging with dry N₂ and compared to those of the same material conditioned over saturated salt solutions. Sepiolite is an important industrial mineral with a modulated structure of alternating tunnels and ribbons. Its mild drying is associated with pronounced vibrational spectral changes due to the removal of surface and zeolitic H₂O and the concomitant structural relaxation of the ribbons. Detailed assignments are provided for the fundamental, combination and overtone spectrum of H₂O confined in the tunnels of sepiolite, SiOH groups on the external surface of the particles, and Mg₃OH groups in the 2:1 ribbons. The spectra are discussed in comparison to those of palygorskite (modulated phyllosilicate with narrower ribbons and tunnels), talc (trioctahedral magnesian phyllosilicate without modulation) and high-surface area silica. It is demonstrated that sepiolite exhibits three discrete states of zeolitic hydration at ambient temperature: Besides the previously known hydrated (w = 7–8) and dry (w = 0–1) states which dominate the spectra above 30% and below 3% relative humidity, respectively, a hitherto unknown intermediate (w = 4–5) is found in the 3–10% range. The new state is most conveniently identified in the near-infrared by a ν₀₂ Mg₃O-H stretching mode at 7205 cm⁻¹ (ν₀₁ = 3686 cm⁻¹, X = 83.5 cm⁻¹) and a characteristic H₂O combination band at 5271 cm⁻¹ (D₂O: 3908 cm⁻¹).     

2-巯基苯并噻唑对铜缓蚀行为的表面增强红外光谱研究

2-巯基苯并噻唑(MBT)是Cu的高效缓蚀剂,但是缓蚀机理存在较大争议.本文通过电化学极化曲线从宏观角度对缓蚀效率进行评估,并利用原位衰减全反射-表面增强红外光谱技术结合理论计算研究了电位控制下的微观吸附构型.结果表明:在较高电位(大于0 V,相对饱和甘汞电极(SCE))下,MBT和金属Cu之间发生电子转移,MBT以硫醇式的环外S和N与金属Cu(I)离子配位在表面形成聚合物膜;在较低电位(小于0 V,vs SCE)下,MBT通过环外S原子以硫醇离子形式在金属Cu表面直立吸附.表面膜阻止了腐蚀介质的侵蚀,起到了较好的缓蚀效果.     

Surface characterization of a cross‐linked cytochrome c film on cysteamine‐modified gold electrodes

The aim of the present paper is to characterize a cross‐linked horse heart cytochrome c (HHC) film on cysteamine‐modified gold electrodes. The HHC film was deposited using 1‐ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide (EDC) as a coupling agent. Attenuated total reflection infrared (ATR‐IR) spectroscopic analyses were performed to characterize the newly formed surface on a qualitative and conformational level. The film thickness was measured using a noncontact optical surface profiler, while quantitative data and information on the heterogeneity of the film were obtained by means of synchrotron radiation X‐ray micro fluorescence (SR micro‐XRF). Results indicate that, in addition to electrochemical studies, spectroscopic analysis methods are essential to gain insight in the effect of immobilization strategies on protein conformations. The latter is of relevance in the development and optimization of biosensors. Copyright © 2009 John Wiley & Sons, Ltd.     

Effects of sampling methodologies on FT-IR data base searching

The sampling methodologies employed in Fourier Transform Infrared (FT-IR) spectroscopy tend to distort to a degree the data obtained relative to that which would be obtained via transmittance. This distortion complicates data base searching. A standard sample of polystyrene was investigated using the techniques of transmittance, attenuated total reflectance (ATR), diffuse reflectance (DRIFT) and photoacoustic spectroscopy (PAS). Several types of corrections are employed to minimize the distortions due to sampling methodologies.These corrections are evaluated with respect to four distinct search algorithms. The results obtained indicate that proper mathematical treatment of the data prior to data base searching enhances the discrimination value of a data base search.     

Analysis of Pathogenic Bacterial and Yeast Biofilms Using the Combination of Synchrotron ATR-FTIR Microspectroscopy and Chemometric Approaches

Biofilms are assemblages of microbial cells, extracellular polymeric substances (EPS), and other components extracted from the environment in which they develop. Within biofilms, the spatial distribution of these components can vary. Here we present a fundamental characterization study to show differences between biofilms formed by Gram-positive methicillin-resistant Staphylococcus aureus (MRSA), Gram-negative Pseudomonas aeruginosa, and the yeast-type Candida albicans using synchrotron macro attenuated total reflectance-Fourier transform infrared (ATR-FTIR) microspectroscopy. We were able to characterise the pathogenic biofilms’ heterogeneous distribution, which is challenging to do using traditional techniques. Multivariate analyses revealed that the polysaccharides area (1200–950 cm⁻¹) accounted for the most significant variance between biofilm samples, and other spectral regions corresponding to amides, lipids, and polysaccharides all contributed to sample variation. In general, this study will advance our understanding of microbial biofilms and serve as a model for future research on how to use synchrotron source ATR-FTIR microspectroscopy to analyse their variations and spatial arrangements.