Study of protein aggregation using two-dimensional correlation infrared spectroscopy and spectral simulations

Research of 2D-COS with metabolomics modifications through deep learning for traceability of wine

To tackle the difficulty of extracting features from one-dimensional spectral signals using traditional spectral analysis, a metabolomics analysis method is proposed to locate two-dimensional correlated spectral feature bands and combine it with deep learning classification for wine origin traceability. Metabolomics analysis was performed on 180 wine samples from 6 different wine regions using UPLC-Q-TOF-MS. Indole, Sulfacetamide, and caffeine were selected as the main differential components. By analyzing the molecular structure of these components and referring to the main functional groups on the infrared spectrum, characteristic band regions with wavelengths in the range of 1000-1400 nm and 1500-1800 nm were selected. Draw two-dimensional correlation spectra (2D-COS) separately, generate synchronous correlation spectra and asynchronous correlation spectra, establish convolutional neural network (CNN) classification models, and achieve the purpose of wine origin traceability. The experimental results demonstrate that combining two segments of two-dimensional characteristic spectra determined by metabolomics screening with convolutional neural networks yields optimal classification results. This validates the effectiveness of using metabolomics screening to determine spectral feature regions in tracing wine origin. This approach effectively removes irrelevant variables while retaining crucial chemical information, enhancing spectral resolution. This integrated approach strengthens the classification model's understanding of samples, significantly increasing accuracy.

Quantitative analysis method of Panax notoginseng based on thermal perturbation terahertz two-dimensional correlation spectroscopy

This paper proposes a Panax notoginseng (P. notoginseng) quantitative analysis based on terahertz time-domain spectroscopy and two-dimensional correlation spectroscopy (2DCOS). By imposing temperature perturbation combined with 2DCOS, the one-dimensional absorbance spectra were transformed into 2DCOS synchronous spectra, which reflected the differences in characteristic information between different P. notoginseng contents more clearly. Then, the feature information of P. notoginseng contents was extracted from the 2DCOS synchronous spectra by a competitive adaptive reweighted sampling (CARS) method and was used to build a quantitative model combined with a support vector regression machine (SVR), called 2DCOS-CARS-SVR. We obtained a more accurate analysis result than the commonly used principal component analysis (PCA)-partial least squares regression (PLSR) and PCA-SVR. The prediction set correlation coefficient and root mean square error reached 0.9915% and 0.8160%, respectively.

Extended application of deep learning combined with 2DCOS: Study on origin identification in the medicinal plant of Paris polyphylla var. yunnanensis

INTRODUCTION

Medicinal plants are very important to human health, and ensuring their quality and rapid evaluation are the current research concerns. Deep learning has a strong ability in recognition. This study extended it to the identification of medicinal plants from the perspective of spectrum.

OBJECTIVE

In order to realise the rapid identification and provide a reference for the selection of high-quality resources of medicinal plants, a combination of deep learning and two-dimensional correlation spectroscopy (2DCOS) was proposed.

METHODS

For the first time, Fourier transform mid-infrared (FT-MIR) and near-infrared (NIR) spectroscopy 2DCOS images combined with residual neural network (ResNet) was used for the origin identification of Paris polyphylla var. yunnanensis. In total 1593 samples were collected and 12821 2DCOS images were drawn. The climate of different origins was briefly analysed.

RESULTS

The xishuangbanna, puer, lincang, honghe and wenshan are the five regions with more ecological advantages. The synchronous 2DCOS models of FT-MIR and NIR could realise origin identification with the accuracy of 100%. The synchronous images were suitable for the identification of medicinal plants with complex systems. The full band, feature band and different contour models had no big difference in distinguishing ability, so they were not the key factors affecting the discrimination results.

CONCLUSION

The ResNet models established were stable, reliable, and robust, which not only solved the problem of origin identification, expanded the application field of deep learning, but also provided practical reference for the related research of other medicinal plants.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.

Binding of aldehydes to myofibrillar proteins as affected by two-step heat treatments

BACKGROUND

The present study investigated the effect of two-step heat treatments on the structure of grass carp myofibrillar proteins (MPs) and their binding ability for selected aldehydes (hexanal, heptanal, octanal and nonanal).

RESULTS

Within 30 min of the first heating step at 40 °C and 5-10 min of the second heating step at 90 °C, the enhancement of the flavor-binding ability was likely explained by the increases in surface hydrophobicity and total sulfhydryl content due to the unfolding of secondary structures of MPs through exposure of hydrophobic amino acids and sulfhydryl groups. Nevertheless, lengthy heating at 90 °C accelerated the aggregation of unfolded MPs and reduced the hydrophobic bonding sites, thus weakening the hydrophobic interactions and decreasing the resultant binding ability of MPs with aldehydes.

CONCLUSION

The binding ability of aldehydes to MPs was found to be strongly influenced by changes in protein structure and surface during the two-step heating process. The results provided insight into improving the flavor characteristics of freshwater fish surimi products. © 2019 Society of Chemical Industry.

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.

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.

The conformation of human phospholipid scramblase 1, as studied by infrared spectroscopy. Effects of calcium and detergent

Human phospholipid scramblase 1 (SCR) is a membrane protein that catalyzes the transmembrane (flip-flop) motion of phospholipids. It can also exist in a non membrane-bound form in the nucleus, where it modulates several aspects of gene expression. Catalysis of phospholipid flip-flop requires the presence of millimolar Ca²⁺, and occurs in the absence of ATP. Membrane-bound SCR contains a C-terminal α-helical domain embedded in the membrane bilayer. The latter domain can be removed giving rise to a stable truncated mutant SCRΔ that is devoid of scramblase activity. In order to improve our understanding of SCR structure infrared spectra have been recorded of both the native and truncated forms, and the effects of adding Ca²⁺, or removing detergent, or thermally denaturing the protein have been observed. Under all conditions the main structural component of SCR/SCRΔ is a β-sheet. Removing the C-terminal 28 aa residues, which anchor SCR to the membrane, leads to a change in tertiary structure and an increased structural flexibility. The main effect of Ca²⁺ is an increase in the α/β ratio of secondary structure components, with a concomitant increase in the proportion of non-periodic structures. At least in SCRΔ, detergent (Zwittergent 3-12) decreases the structural flexibility, an effect somewhat opposite to that of increasing temperature. Thermal denaturation is affected by Ca²⁺, detergent, and by the presence or absence of the C-terminal domain, each of them influencing in different ways the denaturation pattern.

Insight into resolution enhancement in generalized two-dimensional correlation spectroscopy

Generalized two-dimensional correlation spectroscopy (2D-COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D-COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) is not completely understood. In the work here, we studied the 2D-COS of simulated spectra in order to develop new insights into the dependence of 2D-COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We found that the features in the 2D-COS maps that are derived from overlapping bands were determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identified the conditions required to resolve overlapping bands. In particular, 2D-COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands.

2D-SEIRA spectroscopy to highlight conformational changes of the cytochrome c oxidase induced by direct electron transfer

Potentiometric titrations of the cytochrome c oxidase (CcO) immobilized in a biomimetic membrane system were followed by two-dimensional surface-enhanced IR absorption spectroscopy (2D SEIRAS) in the ATR-mode. Direct electron transfer was employed to vary the redox state of the enzyme. The CcO was shown to undergo a conformational transition from a non-activated to an activated state after it was allowed to turnover in the presence of oxygen. Differences between the non-activated and activated state were revealed by 2D SEIRA spectra recorded as a function of potential. The activated state was characterized by a higher number of correlated transitions as well as a higher number of amino acids associated with electron transfer.

Influence of amino acid specificities on the molecular and supramolecular organization of glycine-rich elastin-like polypeptides in water

Elastin-like polypeptides adopt complex supramolecular structures, showing either a hydrophobic or a hydrophilic surface, depending on their surrounding environment and the supporting substrate. The preferred organization is important in many situations ranging from biocompatibility to bio-function. Here we compare the n-repeat pentamer LeuGlyGlyValGly (n = 7) with the analogue ValGlyGlyValGly (n = 5), as water suspensions and as deposits on silicon substrates. These sequences contain the repeat XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) motif belonging to the hydrophobic glycine-rich domain of elastin and represent a simplified model from which to obtain information on molecular interactions functional to elastin itself. The compounds studied differ only by the presence of the -CH(2)- spacer in the Leu moiety and thus the work was aimed at revealing the influence of this spacer element on self assembly. Both polypeptides were studied under identical conditions, using combined techniques, to identify differences in their conformational states both at molecular (CD, FTIR) and supramolecular (XPS, AFM) levels. By these means, together with a Congo Red spectroscopic assay of β-sheet formation in water, a clear correlation between amino acid sequences (sequence specificity) and their kinetics and ordering of aggregation has emerged. The novel outcomes of this work are from the supplementary measurements, made to augment the AFM and XPS studies, showing that the significant step in the self assembly of both polypeptides takes place in the liquid phase and from the finding that the substitution of Val by Leu in the first position of the pentapeptide effectively inhibits the formation of amyloidal fibers.

Solid-State NMR characterization of autofluorescent fibrils formed by the elastin-derived peptide GVGVAGVG

The characterization of the molecular structure and physical properties of self-assembling peptides is an important aspect of optimizing their utility as scaffolds for biomaterials and other applications. Here we report the formation of autofluorescent fibrils by an octapeptide (GVGVAGVG) derived via a single amino acid substitution in one of the hydrophobic repeat elements of human elastin. This is the shortest and most well-defined peptide so far reported to exhibit intrinsic fluorescence in the absence of a discrete fluorophore. Structural characterization by FTIR and solid-state NMR reveals a predominantly β-sheet conformation for the peptide in the fibrils, which are likely assembled in an amyloid-like cross-β structure. Investigation of dynamics and the effects of hydration on the peptide are consistent with a rigid, water excluded structure, which has implications for the likely mechanism of intrinsic fibril fluorescence.

Membranotropic effects of arbidol, a broad anti-viral molecule, on phospholipid model membranes

Arbidol, a broad and potent antiviral molecule, incorporates rapidly into membranes. To gain further insight into the mode of action of Arbidol, since the exact antiviral mechanism of Arbidol is unknown, I examined its interaction and effects on model membranes composed of saturated phospholipids by performing a detailed biophysical study using calorimetry and infrared spectroscopy. Arbidol interacts and modifies the physicochemical properties of the phospholipids in the membrane, having a significant effect on negatively charged phospholipids but a minor one on zwitterionic phospholipids. The data suggest that Arbidol is located at the interface of the membrane, participates in hydrogen bonding either with water or the phospholipid or both, and decreases the hydrogen bonding network of the phospholipids giving place to a phospholipid phase similar to the dehydrated solid one. The significant effects produced on negatively charged phospholipids suggest that the active molecule of Arbidol in the membrane is the protonated one, that is, the positively charged molecule. These data suggest that the potent antiviral effects of Arbidol are mediated at least in part through its membranotropic effects, likely giving place to the formation of perturbed membrane structures. These modifications interfere with proper membrane functioning and should be responsible for its broad antiviral activity.

A membranotropic region in the C-terminal domain of hepatitis C virus protein NS4B interaction with membranes

We have identified a membrane-active region in the HCV NS4B protein by studying membrane rupture induced by a NS4B-derived peptide library on model membranes. This segment corresponds to one of two previously predicted amphipathic helix and define it as a new membrane association domain. We report the binding and interaction with model membranes of a peptide patterned after this segment, peptide NS4B(H2), and show that NS4B(H2) strongly partitions into phospholipid membranes, interacts with them, and is located in a shallow position in the membrane. Furthermore, changes in the primary sequence cause the disruption of the hydrophobicity along the structure and prevent the resulting peptide from interacting with the membrane. Our results suggest that the region where the NS4B(H2) is located might have an essential role in the membrane replication and/or assembly of the viral particle through the modulation of the replication complex. Our findings therefore identify an important region in the HCV NS4B protein which might be implicated in the HCV life cycle and possibly in the formation of the membranous web.

An insight into sequential order in two-dimensional correlation spectroscopy

Determination of the sequential order of events is a very important feature of generalized two-dimensional correlation spectroscopy (2D-COS). Recently, queries have been put forward on the actual effectiveness of this method when changes are non-periodic, particularly in the presence of local sequential order. Consequently, it brings an urgent necessity to understand the true connotation of the sequential order parameter derived from 2D-COS analysis. This article presents an attempt to address these questions based on the analysis of simulated spectra by assuming the band intensity changes in a logarithmic, exponential, hyperbolic, or polynomial manner. It is concluded that for two events changing monotonically and without local sequential orders, one event occurring prior to the other as determined using 2D-COS means in most cases that the former has both a shorter half-time and a greater half-intensity. As a rule of thumb, intensity versus the perturbation factor should be plotted before performing the 2D-COS analysis to determine the sequential order of the involved events. In the presence of obvious local sequential order, 2D-COS analysis is unnecessary. Otherwise, sequential order can be determined quite reliably based on 2D-COS analysis.

Two-dimensional infrared correlation spectroscopy study of the interaction of oxidized and reduced cytochrome c with phospholipid model membranes

We have used two-dimensional infrared correlation spectroscopy (2D-IR) to study the interaction and conformation of cytochrome c in the presence of a binary phospholipid mixture composed of a zwitterionic perdeuterated phospholipid and a negatively-charged one. The influence of the main temperature phase transition of the phospholipid model membranes on the conformation of cytochrome c has been evaluated by monitoring both the Amide I' band of the protein and the CH(2) and CD(2) stretching bands of the phospholipids. Synchronous 2D-IR analysis has been used to determine the different secondary structure components of cytochrome c which are involved in the specific interaction with the phospholipids, revealing the existence of a specific interaction between the protein with cardiolipin-containing vesicles but not with phosphatidic acid-containing ones. Interestingly, 2D-IR is capable of showing the existence of significant changes in the protein conformation at the same time that the phospholipid transition occurs. In summary, 2D-IR revealed an important effect of the phospholipid phase transition of cardiolipin on the secondary structure of oxidized cytochrome c but not to either reduced cytochrome c or in the presence of phosphatidic acid, demonstrating the existence of specific intermolecular interactions between cardiolipin and cytochrome c.

Fe2+-catalyzed non-enzymatic glycosylation alters collagen conformation during AGE-collagen formation in vitro

Advanced glycation end-products (AGEs) are one of the major factors of hyperglycemia related complications for diabetic patients. We studied the formation of AGEs in type I collagen after Fe2+-catalyzed non-enzymatic glycosylation in vitro. Type I collagen isolated from rat tail tendon was incubated with glucose and increasing concentrations of iron ions Fe2+. After 4 weeks incubation, cytotoxity of AGEs was indicated by the cytotoxity assay of primary human umbilical vein endothelial cells and primary human monocytes cultured with glycosylated collagen AGEs. Fourier transform infrared spectroscopy analysis revealed that structural changes of functional groups in glycosylated collagen are accelerated by the catalyst Fe2+. Using two-dimensional Fourier-transform infrared correlation spectroscopy analyses, for the first time, we demonstrated that the order of structural changes of these functional groups is -CH->Amide I>Amide II>Amide III>nu(C=O) the carboxylic group of Asn, Gln or polyproline amino acid residue in the course of AGE-collagen formation. Knowing the positions of these functional groups in collagen, this order of changes indicates that during glycation of collagen, the structure of the main chain residues in collagen changed first, and then the side chain changed gradually, which may lead to more carboxylic groups exposed to glucose for further formation of AGE-collagen irreversibly. The findings presented may support the design of new therapeutic strategies to prevent or slow down the Fe2+-catalyzed glycosylation of collagen and other matrix proteins.

Near-infrared characterization on the secondary structure of regenerated Bombyx mori silk fibroin

Several advantages of the near-infrared (NIR) technique in the characterization of the secondary structure of regenerated Bombyx mori silk fibroin are demonstrated. Silk fibroin films with thicknesses ranging from 50 to 300 microm are suitable for the NIR measurement. The bands due to hydrogen-bonded water are independent in the NIR spectra and facilitate our investigation of the amide region. Analysis of the combination modes of amide groups in the NIR spectra could lead to a profile of conformation ratio of silk fibroin, which was supported by nuclear magnetic resonance (NMR) observations.

Interaction of alcohols with serum LDL

The interaction of low molecular weight alcohols with low density lipoprotein (LDL) has been studied using amide I band-fitting, thermal profiling and two-dimensional infrared correlation spectroscopy (2D-IR). At 0.3 M alcohol, no changes in secondary structure are observed. In the presence of 1 M alcohol, ethanol and propanol decreases protein denaturation temperature and produces changes in the amide I thermal profiles of protein components and in the lipid bands. The 2D-IR synchronous map corresponding to protein or lipid component at 20-37 degrees C suggests differences in the presence of propanol. The asynchronous map corresponding to the lipid component indicates changes in bandwidth, compatible with a more fluid environment. In the 37-80 degrees C temperature range the thermal profile is different in the presence of propanol, both for the lipid and protein components. The results presented show that when alcohols affect the protein component, the lipid spectrum also varies pointing to an effect on the lipid-protein interaction.

Mapping and molecular characterization of novel monoclonal antibodies to conformational epitopes on NH2 and COOH termini of mammalian tryptophanyl-tRNA synthetase reveal link of the epitopes to aggregation and Alzheimer's disease

Tryptophanyl-tRNA synthetase (TrpRS) is an interferon-induced phosphoprotein with autoantigenic and cytokine activities detected in addition to its canonical function in tRNA aminoacylation. The availability of monoclonal antibodies (mAbs) specific for TrpRS is important for development of tools for TrpRS monitoring. A molecular characterization of two mAbs raised in mice, using purified, enzymatically active bovine TrpRS as the inoculating antigen, is presented in this report. These IgG1 antibodies are specific for bovine, human and rabbit but not E. coli TrpRS. Immunoreactivity and specificity of mAbs were verified with purified recombinant hTrpRS expressed in E. coli and TrpRS-derived synthetic peptides. One of the mAbs, 9D7 is able to disaggregate fibrils formed by Ser32-Tyr50 TrpRS-peptide. Epitope mapping revealed that disaggregation ability correlates with binding of 9D7 to this peptide in ELISA and immunocytochemistry. This epitope covers a significant part of N-terminal extension that suggested to be proteolytically deleted in vivo from the full-length TrpRS whereas remaining COOH-fragment possesses a cytokine activity. For epitope mapping of mAb 6C10, the affinity selected phage-displayed peptides were used as a database for prediction of conformational discontinuous epitopes within hTrpRS crystal structure. Using computer algorithm, this epitope is attributed to COOH-terminal residues Asp409-Met425. In immunoblotting, the 6C10 mAb reacts preferably with (i) oligomer than monomer, and (ii) bound than free TrpRS forms. The hTrpRS expression was shown to correlate with growth rates of neuroblastoma and pancreatic cancer cells. Immunohistochemically both mAbs revealed extracellular plaque-like aggregates in hippocampus of Alzheimer's disease brain.

Supramolecular Amyloid-like Assembly of the Polypeptide Sequence Coded by Exon 30 of Human Tropoelastin

Elastin is known to self-aggregate in twisted-rope filaments. However, an ultrastructural organization different from the fibrils typical of elastin, but rather similar to those shown by amyloid networks, is shown by the polypeptide sequence encoded by exon 30 of human tropoelastin. To better understand the molecular properties of this sequence to give amyloid fibers, we used CD, NMR, and FTIR (Fourier transform infrared spectroscopy) to identify the structural characteristics of the peptide. In this study, we have demonstrated, by FTIR, that antiparallel beta-sheet conformation is predominant in the exon 30 fibers. These physical-chemical studies were combined with transmission electron microscopy and atomic force microscopy to analyze the supramolecular structure of the self-assembled aggregate. These studies show the presence of fibrils that interact side-by-side probably originating from an extensive self-interaction of elemental cross beta-structures. Similar sequences, of the general type XGGZG(X, Z = V, L, A, I), are widely found in many proteins such as collagens IV and XVII, major prion protein precursor, amyloid beta A4 precursor protein-binding family, etc., thus suggesting that this sequence could be involved in contributing to the self-assembly of amyloid fibers even in other proteins.