Temperature-dependent near-infrared spectra of bovine serum albumin in aqueous solutions: spectral analysis by principal component analysis and evolving factor analysis

Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules

Principal component analysis (PCA) is used to reduce the dimensionalities of high-dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high-dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods and their applications for investigating protein dynamics.

Insight into the stability of protein in confined environment through analyzing the structure of water by temperature-dependent near-infrared spectroscopy

To understand the stability of protein in confined environment, the near-infrared (NIR) spectra of aqueous solutions and reverse micelles (RMs) containing bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) were measured at different temperature. With the resolution enhanced spectra calculated by continuous wavelet transform (CWT), the intensity change of the α-helix band at 4617 cm^-1 with temperature shows a clear denaturation of the protein in aqueous solution but not in RMs. The effect of the confined environment on the stability of the proteins is indicated. More importantly, the intensity change of the spectral bands of water around 6956 and 6842 cm^-1 provide an evidence for the denaturation, suggesting that water can be a probe exhibiting the structural change of proteins. Furthermore, comparing the spectral features of different water structures obtained by principal component analysis (PCA) from the spectra of RM with and without BSA, it is demonstrated that the bridging water connecting NH in protein and SO in the inner surface of RM may be the reason for the stabilization.

Understanding the effect of urea on the phase transition of poly(N-isopropylacrylamide) in aqueous solution by temperature-dependent near-infrared spectroscopy

Regulating the folding state by denaturants is essential for the structure and function of proteins. Poly(N-isopropyl acrylamide) (PNIPAM) is usually regarded as a model for protein denaturation. The effects of urea, as a denaturant, on the aggregations of PNIPAM was studied by temperature-dependent near-infrared (NIR) spectroscopy, and particularly the variation of water structures was analyzed. The NIR spectra of the polymer-urea solutions containing different polymer concentrations were measured at different temperatures. N-way principal component analysis (NPCA) was performed to observe the spectral information. Three principal components (PCs) containing the spectral information of CH groups were obtained, showing three kinds of CH in the system. Obvious dehydration of the three CH groups occurs at 27.5 °C in solution, but the temperature turns to 27 °C for two kinds of the CH and 26.5 °C for the third one, respectively, in the urea-add solution. The effect of urea on the formation of the intramolecular hydrogen bonds that promotes polymer folding is suggested. The spectral information of NH in urea molecule indicates that the direct interaction of urea and polymer facilitates the stability of the polymer globule state. Furthermore, the spectral information of OH shows that the release of the water molecules with three hydrogen bonds (S₃), which may connect the NH and CO groups in PNIPAM in solution, leads to the phase transition. When urea is added, urea may reduce the content of the S₃ water to facilitate the release, making the phase transition at a low temperature.

Near-Infrared Spectroscopy in Bio-Applications

Near-infrared (NIR) spectroscopy occupies a specific spot across the field of bioscience and related disciplines. Its characteristics and application potential differs from infrared (IR) or Raman spectroscopy. This vibrational spectroscopy technique elucidates molecular information from the examined sample by measuring absorption bands resulting from overtones and combination excitations. Recent decades brought significant progress in the instrumentation (e.g., miniaturized spectrometers) and spectral analysis methods (e.g., spectral image processing and analysis, quantum chemical calculation of NIR spectra), which made notable impact on its applicability. This review aims to present NIR spectroscopy as a matured technique, yet with great potential for further advances in several directions throughout broadly understood bio-applications. Its practical value is critically assessed and compared with competing techniques. Attention is given to link the bio-application potential of NIR spectroscopy with its fundamental characteristics and principal features of NIR spectra.

Aquaphotomics-From Innovative Knowledge to Integrative Platform in Science and Technology

Aquaphotomics is a young scientific discipline based on innovative knowledge of water molecular network, which as an intrinsic part of every aqueous system is being shaped by all of its components and the properties of the environment. With a high capacity for hydrogen bonding, water molecules are extremely sensitive to any changes the system undergoes. In highly aqueous systems-especially biological-water is the most abundant molecule. Minute changes in system elements or surroundings affect multitude of water molecules, causing rearrangements of water molecular network. Using light of various frequencies as a probe, the specifics of water structure can be extracted from the water spectrum, indirectly providing information about all the internal and external elements influencing the system. The water spectral pattern hence becomes an integrative descriptor of the system state. Aquaphotomics and the new knowledge of water originated from the field of near infrared spectroscopy. This technique resulted in significant findings about water structure-function relationships in various systems contributing to a better understanding of basic life phenomena. From this foundation, aquaphotomics started integration with other disciplines into systematized science from which a variety of applications ensued. This review will present the basics of this emerging science and its technological potential.

Water as a probe for serum-based diagnosis by temperature- dependent near-infrared spectroscopy

Diagnosis based on the compositional variation of biological liquids such as serum has drawn much attention. For exploring the potential diagnostic information from serum samples, temperature-dependent near-infrared (NIR) spectroscopy was developed to obtain the spectral change of water reflecting the interactions in serum solution, and chemometric methods were employed to mine the information from the temperature-dependent NIR spectra. The spectra of 68 healthy controls, 42 patients with the type II diabetes and 16 patients with coronary heart disease were measured and analyzed by chemometric calculations. Continuous wavelet transform (CWT) was used to enhance the resolution of the spectra. From the processed spectra, the information of non-hydrogen-bonded (NHB), weakly hydrogen-bonded (WHB) and strongly hydrogen-bonded (SHB) water species was observed. For explaining the variation of the spectra with temperature, two-dimensional (2D) correlation analysis was adopted. A clear difference in SHB/NHB ratio in the synchronous maps was found between the spectra of the patients and the controls. 86.8% of the controls and 98.3% of the patients can be correctly identified. Furthermore, combining the maps of the synchronous and asynchronous analysis, the correlation between SHB and WHB water species was discovered to have an ability to discriminate the patients of diabetes and heart disease with an accuracy of 83.7% and 75.0%, respectively. Therefore, water may be a probe for providing diagnostic information by temperature-dependent NIR spectroscopy.

Understanding the Interaction Between Oligopeptide and Water in Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy

Investigating the interaction between oligopeptide and water is essential for understanding the structure, dynamics and function of proteins. Temperature-dependent near-infrared (NIR) spectroscopy and independent component analysis (ICA) were employed to study the interaction between oligopeptide and water in aqueous solution. The NIR spectra of two homo-oligopeptides, penta-aspartic acid (D₅) and penta-lysine (K₅), in aqueous solution of different concentration were measured at different temperature (30-90 ℃). Independent component analysis was performed to extract the spectral information that changes with temperature. The independent components (ICs) representing the spectral information of NH and CH₂ groups were obtained. Compared with D₅, the two groups in K₅ change significantly at higher temperature. The result may suggest that K₅ has stronger interaction with water than D₅. Moreover, three ICs that contain the spectral information of the water species with no (S₀), one (S₁), and two (S₂) hydrogen-bonds were obtained. It was shown that the spectral intensity of S₀ and S₁ increases while that of S₂ decreases with the temperature, and the changes of oligopeptide solutions are weaker than those of pure water. The results indicate that water structure is sensitive to temperature and the oligopeptide in aqueous solution improves the thermal stability of the water species. When oligopeptide is added, the spectral intensity of S₀ and S₂ decreases and that of S₁ increases for D₅ solution, but the intensity of all the three species decreases for K₅ solution. Furthermore, the concentration effect of K₅ was found to be stronger than D₅. The result may reveal that D₅ combines with water molecule through forming one hydrogen bond but K₅ interacts with water through a different way.

Essentials of Aquaphotomics and Its Chemometrics Approaches

Aquaphotomics is a novel scientific discipline involving the study of water and aqueous systems. Using light-water interaction, it aims to extract information about the structure of water, composed of many different water molecular conformations using their absorbance bands. In aquaphotomics analysis, specific water structures (presented as water absorbance patterns) are related to their resulting functions in the aqueous systems studied, thereby building an aquaphotome-a database of water absorbance bands and patterns correlating specific water structures to their specific functions. Light-water interaction spectroscopic methods produce complex multidimensional spectral data, which require data processing and analysis to extract hidden information about the structure of water presented by its absorbance bands. The process of extracting information from water spectra in aquaphotomics requires a field-specific approach. It starts with an appropriate experimental design and execution to ensure high-quality spectral signals, followed by a multitude of spectral analysis, preprocessing and chemometrics methods to remove unwanted influences and extract water absorbance spectral pattern related to the perturbation of interest through the identification of activated water absorbance bands found among the common, consistently repeating and highly influential variables in all analytical models. The objective of this paper is to introduce the field of aquaphotomics and describe aquaphotomics multivariate analysis methodology developed during the last decade. Through a worked-out example of analysis of potassium chloride solutions supported by similar approaches from the existing aquaphotomics literature, the provided instruction should give enough information about aquaphotomics analysis i.e. to design and perform the experiment and data analysis as well as to represent water absorbance spectral pattern using various forms of aquagrams-specifically designed aquaphotomics graphs. The explained methodology is derived from analysis of near infrared spectral data of aqueous systems and will offer a useful and new tool for extracting data from informationally rich water spectra in any region. It is the hope of the authors that with this new tool at the disposal of scientists and chemometricians, pharmaceutical and biomedical spectroscopy will substantially progress beyond its state-of-the-art applications.

Understanding the function of water during the gelation of globular proteins by temperature-dependent near infrared spectroscopy

Water plays an indispensable role in the gelation of proteins, but its function still remains unclear. In this work, the variation of water species with the structural changes of globular proteins was investigated using temperature-dependent near infrared (NIR) spectroscopy. Ovalbumin (OVA) was used as a model protein, which forms a gel-like structure as the temperature increases through three phases, i.e., phase I (native), phase II (molten globule state), and phase III (gel state). The structural change and the content variation of different water species in the three phases of gelation were analyzed by two-dimensional correlation NIR spectroscopy and Gaussian fitting. A decrease in the water species with two hydrogen bonds (S2) was found and the change follows the same phases as OVA. In the first two phases, the change occurs after those of other water species but in the third phase, the change is faster than that of free water species. The result indicates that in the native and molten globule states, S2 is located in the hydration shell of OVA to maintain the stability of the protein structure, and then in the gel state, high temperature weakens the hydrogen bonding of S2 and leads to the destruction of the hydration shell, making OVA clusters form a gel structure.

Advancements of two dimensional correlation spectroscopy in protein researches

The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.

Numerical modeling of polymorphic transformation of oleic acid via near-infrared spectroscopy and factor analysis

Near-infrared (NIR) spectroscopy as a tool for direct and quantitatively screening the minute polymorphic transitions of bioactive fatty acids was assessed basing on a thermal heating process of oleic acid. Temperature-dependent NIR spectral profiles indicate that dynamical variances of COOH group dominate its γ → α phase transition, while the transition from active α to β phase mainly relates to the conformational transfer of acyl chain. Through operating multivariate curve resolution-alternating least squares with factor analysis, instantaneous contribution of each active polymorph during the transition process was illustrated for displaying the progressive evolutions of functional groups. Calculated contributions reveal that the α phase of oleic acid initially is present at around -18 °C, but sharply grows up around -2.2 °C from the transformation of γ phase and finally disappears at the melting point. On the other hand, the β phase of oleic acid is sole self-generation after melt even it embryonically appears at -2.2 °C. Such mathematical approach based on NIR spectroscopy and factor analysis calculation provides a volatile strategy in quantitatively exploring the transition processes of bioactive fatty acids; meanwhile, it maintains promising possibility for instantaneous quantifying each active polymorph of lipid materials.

Mutual factor analysis for quantitative analysis by temperature dependent near infrared spectra

Temperature dependent near infrared (NIR) spectroscopy has been developed for analyzing multi-component mixtures and understanding the molecular interactions in solutions. In this work, a chemometric method named as mutual factor analysis (MFA) was proposed for the analysis of temperature dependent NIR spectra. The method extracts the common spectral feature contained in the spectra of different temperature or different concentration. The relative quantity of the extracted spectral feature is proportional to the temperature or concentration. From the spectra of water-glucose mixtures, both the spectral variations induced by temperature and concentration are obtained and the variations are correlated with the inducements, respectively, in a very good linearity. Serum samples were used for validation of the method. An acceptable calibration model with a good correlation coefficient (R² = 0.8639) was obtained for glucose measurement. The relative deviations of the measured concentrations from the calibration model are in the range of -18.7-8.52%, which are in a reasonable level for clinical uses. More importantly, the calculations are based on the spectral information of water that has interactions with the analyte. This provides a new way for quantitative analyses of bio-systems.

Two-dimensional correlation spectroscopy in protein science, a summary for past 20years

Two-dimensional correlation spectroscopy (2DCOS) has been widely used to Infrared, Raman, Near IR, Optical Activity (ROA), Vibrational Circular Dichroism (VCD) and Fluorescence spectroscopy. In addition, several new developments, such as 2D hetero-correlation analysis, moving-window two-dimensional (MW2D) correlation, model based correlation (βν and kν correlation analyses) have also well incorporated into protein research. They have been used to investigate secondary structure, denaturation, folding and unfolding changes of protein, and have contributed greatly to the field of protein science. This review provides an overview of the applications of 2DCOS in the field of protein science for the past 20 year, especially to memory our old friend, Dr. Boguslawa Czarnik-Matusewicz, for her great contribution in this research field. The powerful utility of 2DCOS combined with various analytical techniques in protein studies is summarized. The noteworthy developments and perspective of 2DCOS in this field are highlighted finally.

Probing the secondary structure of bovine serum albumin during heat-induced denaturation using mid-infrared fiberoptic sensors

Planar silver halide fiberoptic sensors were used for the first time for studying the mechanism of heating induced bovine serum albumin (BSA) denaturation by deconvoluted infrared attenuated total reflection (IR-ATR) spectra, and two-dimensional correlation spectroscopy (2D-CoS).

Water molecular system dynamics associated with amyloidogenic nucleation as revealed by real time near infrared spectroscopy and aquaphotomics

The formation of amyloid fibrils proceeds via a nucleation-dependent mechanism in which nucleation phase is generally associated with a high free energy resulting in the rate-limiting step. On the basis of this kinetic feature, the nucleation is one of the most crucial phases controlling the pathogenesis of amyloidoses, but little is known about the details of how protein molecules and surrounding environment vary at this stage. Here, we applied near infrared (NIR) spectral monitoring of water structural changes in real time during the nucleation-dependent fibrillation of insulin. Whilst multivariate spectral analysis in the 2050–2350 nm spectral region indicated cross-β formation, characteristic transformations of water structure have been detected in the spectral region 1300–1600 nm corresponding to the first overtone of water OH stretching vibrations. Furthermore, specific water spectral patterns (aquagrams) related to different water molecular conformations have been found along the course of protein nucleation and aggregation. Right in the beginning, dissociation of hydrogen-bonded network in bulk water and coinstantaneous protein and ion hydration were observed, followed by water hydrogen-bonded networks development, presumably forcing the nucleation. These specific transformations of water spectral pattern could be used further as a biomarker for early non-invasive diagnosis of amyloidoses prior to explosive amplification and deposits of amyloid fibrils.

Near-infrared and mid-infrared Fourier transform vibrational circular dichroism of proteins in aqueous solution

Vibrational circular dichroism (VCD) of a series of proteins in H(2)O solution with differing secondary structure are reported for the first time in the near-infrared (NIR) region as well as the NH-stretching region. The Fourier transform (FT) near-infrared (NIR) measurements were carried out between 6000 to 4000 cm(-1). FT-VCD measurements were simultaneously carried out for the mid-infrared (mid-IR) region from 2000 to 800 cm(-1) for direct comparison to VCD in the NIR region. The NIR VCD spectra of proteins show distinct spectral features for different protein structural motifs, indicating a valuable new method to study protein conformations. The principal VCD transitions in the NIR region are two combination bands, the amide A-II and B-II bands, of the amide A and B fundamentals with the amide II fundamental, and the second overtone of the amide II, referred to as the amide 3 x II band. VCD in the amide A and B band region consisting primarily of NH stretching motions were successfully obtained in H(2)O for the first time for an insulin fibril sample. Similar to the enhanced VCD signal observed in amide I and II regions, the amide A and B VCD of insulin fibril shows strong intensity enhancements, providing an additional valuable probe of protein fibril growth and development in solution. The relative sensitivities of the mid-IR, N-H stretching, and NIR regions are discussed.

Self-assembly of ibuprofen and bovine serum albumin-dextran conjugates leading to effective loading of the drug

A simple and green process of simultaneous formation of albumin nanoparticles and encapsulation of hydrophobic drugs in aqueous solution was developed. Bovine serum albumin (BSA)-dextran conjugates were prepared through the Maillard reaction. Ibuprofen was used as a drug model. The solubility of protonated ibuprofen decreases, and then precipitation occurs when the pH of saturated ibuprofen solution is changed from alkali to acidic value. In the presence of the conjugates, a binding of ibuprofen with BSA through hydrophobic and electrostatic interactions can suppress the precipitation of ibuprofen. After a heat treatment, the gelation of BSA results in the formation of nanoparticles and fixing of the ibuprofen in the core. The nanoparticles were characterized with dynamic and static light scattering, zeta-potential, and transmission electron microscopy. The nanoparticles are of spherical shape having a hydrodynamic diameter of about 70 nm. As much as 0.7 unit weight of ibuprofen can be loaded into one unit weight of the conjugates. The dextran conjugated to BSA stabilizes the nanoparticles in aqueous solution.

Analysis of protein structures and interactions in complex food by near-infrared spectroscopy. 1. Gluten powder

The potential of near-infrared (NIR) spectroscopy in detailed food analysis was tested in a model system consisting of gluten powder treated with moisture and heat. Second-derivative transformation and extended multiplicative signal correction were applied for improving the band resolution and removing physical and quantitative spectral variations. Subsequent chemometric analyses gave loading spectra, which were interpreted as spectral effects of altered protein structures, induced by the treatments. Moistening of the gluten powder resulted in shifts and intensity changes in the protein bands, which could be explained by a combination of minor secondary structure changes, water binding, and changed microenvironments of the amino acid side chains. Heat denaturation induced increases at 2209 nm and decreases at 2167-2182 nm, indicating an alpha-helix to beta-sheet transformation, in agreement with the expectations.

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.

Local factor analysis of rank-deficient reaction systems

The analysis of spectral measurement data sets using local factor analysis (LFA) requires the rank of the sub-matrix under study to be equal to the number of absorbing species present in the associated sub-system. However, because of mass balance or kinetic constraints, LFA will fail if local rank deficiency occurs. A local rank deficiency sub-system may be present in a global full-rank reaction system or a rank-deficient one. In this paper, the problems occurring when using window target-testing factor analysis (WTTFA), one type of the LFA methods, in a local rank-deficient situation are shown. A new augmented WTTFA (AWTTFA) is then proposed for the correct use of WTTFA when rank deficiency occurs. Principles of this new method have been demonstrated by a simulated kinetic system and an industrial batch data set.

Application of near-infrared and Fourier transform infrared spectroscopy in the characterization of ligand-induced conformation changes in folate binding protein purified from bovine milk: influence of buffer type and pH

Fourier transform infrared (FT-IR) and near-infrared (NIR) spectroscopy have been applied to detect structural alterations in folate binding protein (FBP) induced by ligation in different buffer types. The amide I region pointed to a beta-sheet to alpha-helix transition upon ligation in acetate and phosphate buffers, and the formation of intermolecular beta-sheet was indicated at pH 5.0, in agreement with a dimerization of FBP taking place at this pH. The ligand-induced changes in the 2100-2300 nm NIR region were significant for FBP in acetate and phosphate buffers of pH 5.0, and the variations were interpreted as secondary structure changes, based on previous assignments of secondary structures to the combination bands in the NIR region. In the case of acetate buffer, variations in the amide combination bands agreed with the amide I analysis, but for the other buffer types some discrepancies were found and explained by side-chain contributions to the NIR, which could reflect the tertiary and quaternary structure differences. NIR spectra of FBP at pH 7.4 and 5.0 revealed contradictory effects on the side chains, reflecting different polymerization events at the two pH values, whereas the amide I region indicated similar changes at the two pH values. Therefore, we suggest that FT-IR and NIR spectroscopy may complement each other, such that the two techniques in combination may give information on all three types of protein conformational changes. While the secondary structure changes are revealed by FT-IR, the tertiary and quaternary structure changes are reflected in the NIR spectra, although the general influence of the latter changes on the NIR spectra remains to be confirmed.

Near-infrared analysis of protein secondary structure in aqueous solutions and freeze-dried solids

Near-infrared spectroscopy (NIR) of various proteins (bovine serum albumin, lysozyme, ovalbumin, gamma-globulin, beta-lactoglobulin, myoglobin, cytochrome-c) was investigated as a possible analytical method of the protein secondary structure in various physical states. The spectra of proteins in aqueous solutions (transmission mode, solvent-compensated) and those in freeze-dried solids (nondestructive diffuse reflection mode) showed several bands at similar frequencies in the combination (4000-5000 cm(-1)) and first overtone (5600-6600 cm(-1)) spectral regions. The normalized second-derivative near-infrared spectra of proteins in aqueous solutions suggested that some bands indicated alpha-helix (4090, 4365-4370, 4615, and 5755 cm(-1)) and beta-sheet (4060, 4405, 4525-4540, 4865, and 5915-5925 cm(-1)) structures. The proteins mostly maintained spectra characteristic of their native structure after freeze-drying, although some reductions in alpha-helical structure and increase in unordered or beta-sheet structures were observed. The near-infrared analysis also showed beta-sheet formation of heat-treated BSA in aqueous solutions and in subsequently freeze-dried solids. The present results thus indicated that the nondestructive near-infrared analysis can be used for the investigation of dehydration-induced changes in protein secondary structures.