Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements

Exploring the binding mechanism and adverse toxic effects of chiral phenothrin to human serum albumin: Based on multi-spectroscopy, biochemical and computational approach

To understand the binding mechanism of a mixture of chiral phenothrin with human serum albumin (HSA), we used multi-spectroscopy, including steady-state fluorescence spectroscopic titration, three-dimensional fluorescence spectroscopy, circular dichroism, and FTIR spectra to explore the precise interactions between the complex. Based on the modified Stern-Volmer equation, the binding constant (K_a) was calculated under three temperatures, which revealed that phenothrin interacts with HSA through a static quenching mechanism. The thermodynamic parameters including enthalpy change (ΔH) and entropy change (ΔS) were determined by fitting the experimental data with van't Hoff equation, which indicates that electrostatic force and hydrogen bonds dominate the interplay in the phenothrin-HSA complex. Circular dichroism and FTIR showed the addition of phenothrin changed the secondary structure of proteins, in which the α-helicity decreased from 52.37% in free HSA to 50.02%. The esterase-like activity was reduced with the increase of phenothrin concentration, which may be attributed to the perturbated senior structure of HSA. Competitive displacement experiments confirmed that phenothrin inserted into the subdomain IIA (site I) of HSA. Several computational approaches such as molecular docking, frontier molecular orbital analysis, and electrostatic potential analysis were utilized to probe into the binding mode of the phenothrin-HSA complex. The binding behaviors of the chiral phenothrin mixture differed during the complexation. In conclusion, both the experimental and theoretical investigations provide useful information for better understanding and reducing the potential deleterious effects of the chiral phenothrin mixture on human long-term physio-pathological status.

ATR-FTIR Biosensors for Antibody Detection and Analysis

Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level.

Spectroscopic investigation of conformational changes in urease caused by interaction with humic acid

Urease in soil interacts with humic acid (HA), which results in a change of the enzymatic activity and stability. However, knowledge on the conformational change of urease in the presence of HA is still lacking. Therefore, the structure of urease (net zero charge at pH 5.2) interacting with HA and the microenvironments of the tyrosine (Tyr) and tryptophane (Trp) residues were investigated at pH 6.7 and 8.0 and 0.5 and 50 mmol L^-1 KCl using spectroscopic techniques. Fluorescence intensity of urease was progressively inhibited by HA with increasing mass ratio f of HA/urease. Moreover, quenching of urease fluorescence by HA was strongest at pH 6.7 (and 50 mmol L^-1 KCl) where the hydrophobic attraction was counteracted by only a weak electrostatic repulsion. HA exerted only a minor effect on the positions of the maximum excitation bands for Tyr and Trp residues, indicating insignificant changes in the microenvironment of these residues in the presence of HA. At pH 6.7, the amide I and amide II bands were inhibited by HA. Curve-fitting of the amide I band of urease in complexes indicated that the percentages of α-helix, β-sheet and β-turn were changed. At pH 8 HA had little effect on the circular dichroism and attenuated total reflectance Fourier transform infrared spectra of urease. At this pH the interaction between urease and HA was weak due to the relatively strong electrostatic repulsion and the conformational change was insignificant. The present results increase our understanding of negatively charged protein behavior in natural environments dominated by humic substances.

Broadband laser-based mid-IR spectroscopy for analysis of proteins and monitoring of enzyme activity

Laser-based infrared (IR) spectroscopy is an emerging key technology for the analysis of solutes and for real-time reaction monitoring in liquids. Larger applicable pathlengths compared to the traditional gold standard Fourier transform IR (FTIR) spectroscopy enable robust measurements of analytes in a strongly absorbing matrix such as water. Recent advancements in laser development also provide large accessible spectral coverage thus overcoming an inherent drawback of laser-based IR spectroscopy. In this work, we benchmark a commercial room temperature operated broadband external cavity-quantum cascade laser (EC-QCL)-IR spectrometer with a spectral coverage of 400 cm^-1 against FTIR spectroscopy and showcase its application for measuring the secondary structure of proteins in water, and for monitoring the lipase-catalyzed saponification of triacetin. Regarding the obtained limit of detection (LOD), the laser-based spectrometer compared well to a research-grade FTIR spectrometer employing a liquid nitrogen cooled detector. With respect to a routine FTIR spectrometer equipped with a room temperature operated pyroelectric detector, a 15-fold increase in LOD was obtained in the spectral range of 1600-1700 cm^-1. Characteristic spectral features in the amide I and amide II region of three representative proteins with different secondary structures could be measured at concentrations as low as 0.25 mg mL^-1. Enzymatic hydrolysis of triacetin by lipase was monitored, demonstrating the advantage of a broad spectral coverage for following complex chemical reactions. The obtained results in combination with the portability and small footprint of the employed spectrometer opens a wide range of future applications in protein analysis and industrial process control, which cannot be readily met by FTIR spectroscopy without recurring to liquid nitrogen cooled detectors.

FTIR Imaging of Protein Microarrays for High Throughput Secondary Structure Determination

The paper introduces a new method designed for high-throughput protein structure determination. It is based on spotting proteins as microarrays at a density of ca. 2000-4000 samples per cm² and recording Fourier transform infrared (FTIR) spectra by FTIR imaging. It also introduces a new protein library, called cSP92, which contains 92 well-characterized proteins. It has been designed to cover as well as possible the structural space, both in terms of secondary structures and higher level structures. Ascending stepwise linear regression (ASLR), partial least square (PLS) regression, and support vector machine (SVM) have been used to correlate spectral characteristics to secondary structure features. ASLR generally provides better results than PLS and SVM. The observation that secondary structure prediction is as good for protein microarray spectra as for the reference attenuated total reflection spectra recorded on the same samples validates the high throughput microarray approach. Repeated double cross-validation shows that the approach is suitable for the high accuracy determination of the protein secondary structure with root mean square standard error in the cross-validation of 4.9 ± 1.1% for α-helix, 4.6 ± 0.8% for β-sheet, and 6.3 ± 2.2% for the "other" structures when using ASLR.

Multispectral and molecular modeling investigations on the binding behaviors of two anticoccidials with serum albumins

The interaction properties of monensin/clopidol with bovine/human serum albumin (BSA/HSA) were determined via multispectral together with molecular modeling techniques in the report. Fluorescence quenching spectra at different temperatures and fluorescence lifetime determination demonstrated that the fluorescence quenching belonged to a static quenching type. In the case of monensin-BSA, clopidol-BSA, monensin-HSA and clopidol-HSA, the binding constants K_a (291 K) were 5.42 × 10⁴, 4.96 × 10⁴, 3.22 × 10⁴ and 2.99 × 10⁴ M^-1, respectively; the binding distances r₀ were 1.88, 2.53, 2.19 and 2.02 nm, respectively. Monensin and clopidol bound strongly with BSA/HSA with binding free energies equal to -26.37/-25.11 and -26.11/-24.93 kJ mol^-1, respectively. The spontaneous binding process was dominated by hydrogen bonds and van der Waals forces as reflected in thermodynamic parameters analyses. Synchronous, CD, FTIR and UV-vis spectra assays confirmed that serum albumins conformations were altered. Using competitive experiment, monensin/clopidol was observed to bind at site I of serum albumins, which were reconfirmed by the results of molecular modeling.Communicated by Ramaswamy H. Sarma.

Assessment on the binding characteristics of residual marbofloxacin in animal-derived food to bovine/human serum albumin by spectroscopy and molecular modelling

To assess the toxicity of residual marbofloxacin from animal-derived food, the interaction characteristics of marbofloxacin to bovine/human serum albumins (BSA/HSA) were explored using spectroscopic methods combined with molecular modelling. According to fluorescence spectra and time-resolved fluorescence spectra measurements, quenching of BSA/HSA fluorescence induced by marbofloxacin was characterized as static quenching. A 1:1 ground-state complex of marbofloxacin to BSA/HSA was formed with binding constant (K_a ) 1.66 × 10⁴ /9.74 × 10³ M^-1 at 291 K. The location of marbofloxacin binding at site I within BSA/HSA was clarified by site marker competitive experiments. Molecular modelling demonstrated that the binding region for marbofloxacin to BSA and HSA were at site I with the lowest binding free energies of -22.86 and -21.60 kJ mol^-1 , respectively. Hydrogen bonds and van der Waals forces were dominantly involved in the spontaneous binding. Nonradiation energy transferred from BSA and HSA to marbofloxacin, due to the close distance (r₀ ) between marbofloxacin and Trp residues of BSA (4.28 nm) and HSA (3.34 nm). As explained by circular dichroism (CD) spectra, an increased BSA/HSA α-helix structure was observed after binding to marbofloxacin. Ultraviolet-visible (UV-vis) and Fourier transform infrared (FT-IR) spectra suggested that conformation of the two proteins was altered by marbofloxacin.

Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration

FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

The Next Generation of IR Spectroscopy: EC-QCL-Based Mid-IR Transmission Spectroscopy of Proteins with Balanced Detection

We report a mid-IR transmission setup for the analysis of the protein amide I and amide II band in aqueous solutions that achieves a limit of detection as low as 0.0025 mg mL-1 (outperforming our previous results and other state-of-the-art mid-IR-based techniques by almost an order of magnitude). This large improvement is made possible by combining the latest-generation external cavity-quantum cascade laser (EC-QCL) operated at room temperature with an optimized double-beam optical setup that adjusts the path length (26 μm) to ensure robust sample handling. For minimizing the noise introduced by the high-intensity laser light source, a thermoelectrically cooled mercury cadmium telluride balanced detection module was employed. In this way, noise levels better by a factor of up to 20 were achieved compared with single-channel measurements. Characteristic spectral features of proteins with different secondary structures were successfully identified at concentrations as low as 0.1 mg mL-1. Furthermore, a highly linear response was demonstrated for concentrations between 0.05 and 10 mg mL-1. The total acquisition time of the setup can be adapted to fulfill the required sensitivity of the protein measurements and to ensure maximum flexibility for future applications. The presented setup combines high sensitivity, large optical path lengths, and short measurement times and thus outperforms previous research type EC-QCL setups as well as commercially available instruments. This opens a wide range of future applications including protein-ligand interaction studies as well as qualitative and quantitative analyses of proteins in complex matrices such as those found in up- and downstream bioprocess monitoring and similar challenging applications which can not be readily met by conventional FT-IR spectroscopy.

pH titration of β-lactoglobulin monitored by laser-based Mid-IR transmission spectroscopy coupled to chemometric analysis

A novel external cavity-quantum cascade laser (EC-QCL)-based setup for mid-IR transmission spectroscopy in the amide I and amide II region was employed for monitoring pH-induced changes of protein secondary structure. pH titration of β-lactoglobulin revealed unfolding of the native β-sheet secondary structure occurring at basic pH. Chemometric analysis of the dynamic IR spectra was performed by multivariate curve resolution-alternating least squares (MCR-ALS). Using this approach, spectral and abundance distribution profiles of the conformational transition were obtained. A proper post-processing procedure was implemented allowing to extract information about pure protein spectra and spurious signals that may interfere in the interpretation of the system. This work demonstrates the potential and versatility of the EC-QCL-based IR transmission setup for flow-through applications, benefitting from the high available optical path length.

Vectofusin-1, a potent peptidic enhancer of viral gene transfer forms pH-dependent α-helical nanofibrils, concentrating viral particles

Gene transfer using lentiviral vectors has therapeutic applications spanning from monogenic and infectious diseases to cancer. Such gene therapy has to be improved by enhancing the levels of viral infection of target cells and/or reducing the amount of lentivirus for greater safety and reduced costs. Vectofusin-1, a recently developed cationic amphipathic peptide with a pronounced capacity to enhance such viral transduction, strongly promotes the entry of several retroviral pseudotypes into target cells when added to the culture medium. To clarify the molecular basis of its action the peptide was investigated on a molecular and a supramolecular level by a variety of biophysical approaches. We show that in culture medium vectofusin-1 rapidly forms complexes in the 10 nm range that further assemble into annular and extended nanofibrils. These associate with viral particles allowing them to be easily pelleted for optimal virus-cell interaction. Thioflavin T fluorescence, circular dichroism and infrared spectroscopies indicate that these fibrils have a unique α-helical structure whereas most other viral transduction enhancers form β-amyloid fibrils. A vectofusin-1 derivative (LAH2-A4) is inefficient in biological assays and does not form nanofibrils, suggesting that supramolecular assembly is essential for transduction enhancement. Our observations define vectofusin-1 as a member of a new class of α-helical enhancers of lentiviral infection. Its fibril formation is reversible which bears considerable advantages in handling the peptide in conditions well-adapted to Good Manufacturing Practices and scalable gene therapy protocols.

Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-l-lysine monitored by FT-IR spectroscopy

Temperature-induced conformational transitions of poly-l-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10°C and 70°C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I' and amide II' spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

On the Identification of Rayon/Viscose as a Major Fraction of Microplastics in the Marine Environment: Discrimination between Natural and Manmade Cellulosic Fibers Using Fourier Transform Infrared Spectroscopy

This work was sparked by the reported identification of man-made cellulosic fibers (rayon/viscose) in the marine environment as a major fraction of plastic litter by Fourier transform infrared (FT-IR) transmission spectroscopy and library search. To assess the plausibility of such findings, both natural and man-made fibers were examined using FT-IR spectroscopy. Spectra acquired by transmission microscopy, attenuated total reflection (ATR) microscopy, and ATR spectroscopy were compared. Library search was employed and results show significant differences in the identification rate depending on the acquisition method of the spectra. Careful selection of search parameters and the choice of spectra acquisition method were found to be essential for optimization of the library search results. When using transmission spectra of fibers and ATR libraries it was not possible to differentiate between man-made and natural fibers. Successful differentiation of natural and man-made cellulosic fibers has been achieved for FT-IR spectra acquired by ATR microscopy and ATR spectroscopy, and application of ATR libraries. As an alternative, chemometric methods such as unsupervised hierarchical cluster analysis, principal component analysis, and partial least squares-discriminant analysis were employed to facilitate identification based on intrinsic relationships of sample spectra and successful discrimination of the fiber type could be achieved. Differences in the ATR spectra depending on the internal reflection element (Ge versus diamond) were observed as expected; however, these did not impair correct classification by chemometric analysis. Moreover, the effects of different levels of humidity on the IR spectra of natural and man-made fibers were investigated, too. It has been found that drying and re-humidification leads to intensity changes of absorption bands of the carbohydrate backbone, but does not impair the identification of the fiber type by library search or cluster analysis.

Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot

Infrared (IR) spectra from 1200 to 1800 cm(-1) of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions.

FTIR spectral signature of anticancer drugs. Can drug mode of action be identified?

Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Studies on the binding of fulvic acid with transferrin by spectroscopic analysis

Transferrin has shown potential in the delivery of anticancer drugs into primarily proliferating cancer cells that over-express transferrin receptors. Fulvic acid has a wide range of biological and pharmacological activities which caused widespread concerns, the interaction of fulvic acid with human serum transferrin (Tf) has great significance for gaining a deeper insight about anticancer activities of fulvic acid. In this study, the mechanism of interaction between fulvic acid and Tf, has been investigated by using fluorescence quenching, thermodynamics, synchronous fluorescence and circular dichroism (CD) under physiological condition. Our results have shown that fulvic acid binds to Tf and form a new complex, and the calculated apparent association constants are 5.04×10(8) M(-1), 5.48×10(7) M(-1), 7.38×10(6) M(-1) from the fluorescence quenching at 288 K, 298 K, and 310 K. The thermodynamic parameters indicate that hydrogen bonding and weak van der Waals are involved in the interaction between fulvic acid and Tf. The binding of fulvic acid to Tf causes the α-helix structure content of the protein to reduce, and resulting that peptide chains of Tf become more stretched. Our results have indicated a mechanism of the interaction between fulvic acid and Tf, which may provide information for possible design of methods to deliver drug molecules via transferrin to target tissues and cells effectively.

Combined dynamic light scattering and Raman spectroscopy approach for characterizing the aggregation of therapeutic proteins

Determination of the physicochemical properties of protein therapeutics and their aggregates is critical for developing formulations that enhance product efficacy, stability, safety and manufacturability. Analytical challenges are compounded for materials: (1) that are formulated at high concentration, (2) that are formulated with a variety of excipients, and (3) that are available only in small volumes. In this article, a new instrument is described that measures protein secondary and tertiary structure, as well as molecular size, over a range of concentrations and formulation conditions of low volume samples. Specifically, characterization of colloidal and conformational stability is obtained through a combination of two well-established analytical techniques: dynamic light scattering (DLS) and Raman spectroscopy, respectively. As the data for these two analytical modalities are collected on the same sample at the same time, the technique enables direct correlation between them, in addition to the more straightforward benefit of minimizing sample usage by providing multiple analytical measurements on the same aliquot non-destructively. The ability to differentiate between unfolding and aggregation that the combination of these techniques provides enables insights into underlying protein aggregation mechanisms. The article will report on mechanistic insights for aggregation that have been obtained from the application of this technique to the characterization of lysozyme, which was evaluated as a function of concentration and pH.

Application of supervised Kohonen map and counter propagation neural network for classification of nucleic acid structures based on their circular dichroism spectra

One of the most popular instrumental methods to detect the DNA structure is circular dichroism. Specific experimental conditions are required to form different structures of DNA. However, there is the possibility of different structures establishing in the similar circumstance. So, methods development to improve the classification and prediction of structures using their spectra information are needed. To this end, we applied unsupervised (PCA) and supervised (PLS-DA, SKN, and CPNN) approaches to classify CD spectra dataset of different DNA sequences (random coil (ss-DNA), duplex, hairpin, reversed and normal triplex, parallel and antiparallel G-quadruplex, and i-motif). The main part of this work concentrates on the application of artificial neural networks and weight analysis to obtain more classification and prediction accuracy. For this purpose, the trained network was run 10 times, and the average weights were taken. Also, weight analysis was done for the prediction of mixture samples include different structures. The results prove that new method of weights analysis based on SKN and CPNN is useful for classification of complicated data such as different types of DNA structures.

Multi-spectroscopic analysis and molecular modeling on the interaction of curcumin and its derivatives with human serum albumin: a comparative study

The comparative study about the interaction between curcumin and its derivatives (demothxycurcumin and bisdeoxycurcumin) with human serum albumin (HSA) has been carried out using multi-spectroscopic analysis and molecular modeling method. The characteristic of fluorescence quenching and the thermodynamic parameters have been studied by state emission fluorescence experiments under different temperatures with an interval of 6 K. Curcumin shows largest quenching constant and bisdeoxycurcumin shows the smallest at the temperature of 298 K. However, the quenching constant of curcumin drops quickly with the increase of temperature. Demothxycurcumin gives the largest quenching efficiency at the temperature of 310 K. An average distance of 6.7 nm for energy transfer has been determined based on förster resonance energy theory (FRET). The site competitive replacement experiments illustrate three compounds mainly binding on site I (Subdomain IIA) of the protein, and show tendency of binding on site II (Subdomain IIIA) with the removing of methoxyl groups. Circular dichroism spectra and Fourier transform infrared spectroscopy (FTIR) have been used to investigate the influence on protein secondary structure. Content of the α-helix increases at low concentrations of the compounds, while unfolding occurs at high concentrations. Docking simulation reveals possible mechanism for different quenching behavior and binding sites preferred by three compounds. The binding modes have effectively supported the conclusion of the experiments.

Change in the microenvironment of breast cancer studied by FTIR imaging

Fourier transform infrared (FTIR) imaging was applied on histopathological specimens of breast cancer of different tumor histological grades. Focus was given to the extracellular matrix. FTIR spectral changes were observed when examining the extracellular matrix close to and far from carcinoma. Major changes were observed, in particular in the relative intensities of the collagen bands at 1640 and 1630 cm(-1). PCA analysis and global fitting indicate a continuous progression in collagen spectral features when moving away from the tumor. These preliminary results suggest FTIR spectral features present in the 1700-1600 cm(-1) spectral range could be used as spectral markers to identify cancer-induced modifications in collagen. This chemical imaging approach to analyze the breast cancer microenvironment could be used in the future for improving diagnostics of breast cancer.

Overestimated accuracy of circular dichroism in determining protein secondary structure

Circular dichroism (CD) is a spectroscopic technique widely used for estimating protein secondary structures in aqueous solution, but its accuracy has been doubted in recent work. In the present paper, the contents of nine globular proteins with known secondary structures were determined by CD spectroscopy and Fourier transform infrared spectroscopy (FTIR) in aqueous solution. A large deviation was found between the CD spectra and X-ray data, even when the experimental conditions were optimized. The content determined by FTIR was in good agreement with the X-ray crystallography data. Therefore, CD spectra are not recommended for directly calculating the content of a protein's secondary structure.

Comparative studies on the interaction of genistein, 8-chlorogenistein, and 3',8-dichlorogenistein with bovine serum albumin

Chlorination can significantly enhance the antioxidant and antitumor activity of genistein. In this paper, genistein, 8-chlorogenistein, and 3',8-dichlorogenistein were selected to investigate the binding to bovine serum albumin (BSA) using fluorescence spectroscopy and circular dichroism (CD). The results showed that chlorination, especially at position 3', had significant effects on the binding constant value of chlorinated genistein derivatives to BSA; however, the binding site and the binding number were slightly affected. The thermodynamic parameters indicated that hydrophobic and electrostatic forces played important roles in the binding process and the enhanced binding affinity mainly associated with the increase of the hydrophobicity caused by the chlorine atom substitution. Furthermore, the CD data demonstrated that the conformation of BSA was slightly altered in the presence of genistein, 8-chlorogenistein, and 3',8-dichlorogenistein, with different reduced α-helix contents. The results obtained herein will be of biological significance in toxicology investigation and genistein derivative drug design.

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms.

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.

Probing the binding sites and the effect of berbamine on the structure of bovine serum albumin

Berbamine, a naturally occurring isoquinoline alkaloid extracted from Berberis sp., is the active constituent of some Chinese herbal medicines and exhibits a variety of pharmacological activities. The effects of berbamine on the structure of bovine serum albumin (BSA) were investigated by circular dichroism, fluorescence and absorption spectroscopy under physiological conditions. Berbamine caused a static quenching of the intrinsic fluorescence of BSA, and the quenching data were analyzed by application of the Stern-Volmer equation. There was a single primary berbamine-binding site on BSA with a binding constant of 2.577x10(4)Lmol(-1) at 298K. The thermodynamic parameters, enthalpy change (DeltaH(0)) and entropy change (DeltaS(0)) for the reaction were -76.5kJmol(-1) and -173.4Jmol(-1)K(-1) according to the van't Hoff equation. The results showed that the hydrogen bond and van der Waals interaction were the predominant forces in the binding process. Competitive experiments revealed a displacement of warfarin by berbamine, indicating that the binding site was located at Drug sites I. The distance r between the donor (BSA) and the acceptor (berbamine) was obtained according to the Förster non-radiation energy transfer theory. The results of three-dimensional fluorescence spectra, UV-vis absorption difference spectra and circular dichroism of BSA in the presence of berbamine showed that the conformation of BSA was changed. The results provide a quantitative understanding of the effect of berbamine on the structure of bovine serum albumin, providing a useful guideline for further drug design.

Multivariate analysis of standoff laser-induced breakdown spectroscopy spectra for classification of explosive-containing residues

A technique being evaluated for standoff explosives detection is laser-induced breakdown spectroscopy (LIBS). LIBS is a real-time sensor technology that uses components that can be configured into a ruggedized standoff instrument. The U.S. Army Research Laboratory has been coupling standoff LIBS spectra with chemometrics for several years now in order to discriminate between explosives and nonexplosives. We have investigated the use of partial least squares discriminant analysis (PLS-DA) for explosives detection. We have extended our study of PLS-DA to more complex sample types, including binary mixtures, different types of explosives, and samples not included in the model. We demonstrate the importance of building the PLS-DA model by iteratively testing it against sample test sets. Independent test sets are used to test the robustness of the final model.

Study of thermal dynamics of defatted bovine serum albumin in D2O solution by Fourier transform infrared spectra and evolving factor analysis

Fourier transform infrared (FT-IR) spectra have been measured for defatted bovine serum albumin (BSA) in D(2)O with a concentration of 2.0 wt % over a temperature range of 26-90 degrees C and the corresponding difference spectra have been calculated by subtracting the contribution of D(2)O at the same temperature. Evolving factor analysis (EFA) by selecting two factors and three factors has been employed to analyze the temperature-dependent difference IR spectra in the 1700-1600 cm(-1) spectral region of the defatted BSA in D(2)O solution. Three-factor EFA has been employed to determine the distinction of the three protein species involved in the process of temperature elevation: native, transitional, and denatured protein. The temperature profiles obtained from three-factor EFA indicate that heat-induced conformational change in the secondary structures of defatted BSA in D(2)O undergoes two two-state transitions, a drastic transition and a slight transition, which occur in the temperature ranges of 68-82 degrees C and 56-76 degrees C, respectively.

Drug characterization in low dosage pharmaceutical tablets using Raman microscopic mapping

Raman micro-spectroscopic mapping is utilized to analyze pharmaceutical tablets containing a low concentration (0.5% w/w) of active pharmaceutical ingredient (API). The domain sizes and spatial distributions of the API and the major excipients are obtained. Domain size of the API is found to be dependent upon the particle size distribution of the ingoing API material, making the Raman maps good indicators of the source of API used in tablet manufacturing. Multivariate classification was performed to simultaneously check for the presence of two undesired API polymorphs within tablets. Raman mapping was demonstrated capable of detecting in the tablet matrix as little as 10% form conversion of the low-dosage (0.5% w/w) API, which is equivalent to detection of a 0.05% w/w polymorphic impurity. Overall, the information provided by Raman micro-spectroscopic mapping was found to have potential utility for manufacturing process optimization or predictive stability assessments.