Detection of the site of phosphorylation in a peptide using Raman spectroscopy and partial least squares discriminant analysis

Vibrational Study on Structure and Bioactivity of Protein Fibers Grafted with Phosphorylated Methacrylates

In the last decades, silk fibroin and wool keratin have been considered functional materials for biomedical applications. In this study, fabrics containing silk fibers from Bombyx mori and Tussah silk fibers from Antheraea pernyi, as well as wool keratin fabrics, were grafted with phosmer CL and phosmer M (commercial names, i.e., methacrylate monomers containing phosphate groups in the molecular side chain) with different weight gains. Both phosmers were recently proposed as flame retarding agents, and their chemical composition suggested a possible application in bone tissue engineering. IR and Raman spectroscopy were used to disclose the possible structural changes induced by grafting and identify the most reactive amino acids towards the phosmers. The same techniques were used to investigate the nucleation of a calcium phosphate phase on the surface of the samples (i.e., bioactivity) after ageing in simulated body fluid (SBF). The phosmers were found to polymerize onto the biopolymers efficiently, and tyrosine and serine underwent phosphorylation (monitored through the strengthening of the Raman band at 1600 cm-1 and the weakening of the Raman band at 1400 cm-1, respectively). In grafted wool keratin, cysteic acid and other oxidation products of disulphide bridges were detected together with sulphated residues. Only slight conformational changes were observed upon grafting, generally towards an enrichment in ordered domains, suggesting that the amorphous regions were more prone to react (and, sometimes, degrade). All samples were shown to be bioactive, with a weight gain of up to 8%. The most bioactive samples contained the highest phosmers amounts, i.e., the highest amounts of phosphate nucleating sites. The sulphate/sulphonate groups present in grafted wool samples appeared to increase bioactivity, as shown by the five-fold increase of the IR phosphate band at 1040 cm-1.

Elucidating the Calcium-Binding Site, Absorption Activities, and Thermal Stability of Egg White Peptide-Calcium Chelate

With the current study, we aimed to determine the characteristics and calcium absorption capacity of egg white peptide-calcium complex (EWP-Ca) and determine the effect of sterilization on EWP-Ca to study the possibility of EWP-Ca as a new potential calcium supplement. The results of SEM and EDS showed a high calcium chelating ability between EWP and calcium, and the structure of EWP-Ca was clustered spherical particles due its combination with calcium. The FTIR and Raman spectrum results showed that EWP could chelate with calcium by carboxyl, phosphate, and amino groups, and peptide bonds may also participate in peptide-calcium binding. Moreover, the calcium absorption of EWP-Ca measured by the intestinal everted sac model in rats was 32.38 ± 6.83 μg/mL, significantly higher than the sample with CaCl2, and the mixture of EWP and Ca (p < 0.05) revealed appropriate calcium absorption capacity. The fluorescence spectra and CD spectra showed that sterilization caused a decrease in the content of α-helix and β-sheet and a significant increase in β-turn (p < 0.05). Sterilization changed the EWP-Ca structure and decreased its stability; the calcium-binding capacity of EWP-Ca after sterilization was decreased to 41.19% (p < 0.05). Overall, these findings showed that EWP could bind with calcium, form a peptide-calcium chelate, and serve as novel carriers for calcium supplements.

A Phosphatase-Mimetic Nano-Stabilizer of Mast Cells for Long-Term Prevention of Allergic Disease

Allergic diseases are pathological immune responses with significant morbidity, which are closely associated with allergic mediators as released by allergen-stimulated mast cells (MCs). Prophylactic stabilization of MCs is regarded as a practical approach to prevent allergic diseases. However, most of the existing small molecular MC stabilizers exhibit a narrow therapeutic time window, failing to provide long-term prevention of allergic diseases. Herein, ceria nanoparticle (CeNP-) based phosphatase-mimetic nano-stabilizers (PMNSs) with a long-term therapeutic time window are developed for allergic disease prevention. By virtue of the regenerable catalytic hotspots of oxygen vacancies on the surface of CeNPs, PMNSs exhibit sustainable phosphatase-mimetic activity to dephosphorylate phosphoproteins in allergen-stimulated MCs. Consequently, PMNSs constantly modulate intracellular phospho-signaling cascades of MCs to inhibit the degranulation of allergic mediators, which prevents the initiation of allergic mediator-associated pathological responses, eventually providing protection against allergic diseases with a long-term therapeutic time window.

Accurate Identification of Human Phosphorylated Proteins by Ensembling Supervised Kernel Self-organizing Maps

Protein phosphorylation is a vital physiological process, which plays a critical role in controlling survival differentiation, cell growth, metabolism and apoptosis. The accurate identification of whether a protein will be phosphorylated solely from protein sequence is especially useful for both basic research and drug development. In this study, a new predictor specifically designed for the prediction of human phosphorylated proteins is proposed. The proposed method first train two supervised kernel self-organizing maps (SKSOMs): one is trained with feature from protein physiochemical composition view, while the other is trained with feature from protein evolutionary information view. Then, the two trained SKSOMs are ensembled to perform the final prediction. Rigorous computational experiments show that the proposed method achieves 78.75 % and 0.561 on ACC and MCC, which are 6.96 % and 12.5 % higher than that of the state-of-the-art predictor. Overall, the study demonstrated a new sensitive avenue to identify human phosphorylated proteins and could be readily extended to recognize phosphorylated proteins for other species.

Conformational Evolution of Molecular Signatures during Amyloidogenic Protein Aggregation

Aggregation is a pathological hallmark of proteinopathies such as Alzheimer's disease and results in the deposition of β-sheet-rich amyloidogenic protein aggregates. Such proteinopathies can be classified by the identity of one or more aggregated proteins, with recent evidence also suggesting that distinct molecular conformers (strains) of the same protein can be observed in different diseases, as well is in subtypes of the same disease. Therefore, methods for the quantification of pathological changes in protein conformation are central to understanding and treating proteinopathies. In this work, the evolution of Raman spectroscopic molecular signatures of three conformationally distinct proteins, bovine serum albumin (α-helical-rich), β2-microglobulin (β-sheet-rich), and tau (natively disordered), was assessed during aggregation into oligomers and fibrils. The morphological evolution was tracked using atomic force microscopy and corresponding conformational changes were assessed by their Raman signatures acquired in both wet and dried conditions. A deconvolution model was developed which allowed us to quantify the conformation of the nonregular protein tau, as well as for the oligomeric and fibrillar species of each of the proteins. Principle component analysis of the fingerprint region allowed further identification of the distinguishing spectral features and unsupervised distinction. While an increase in β-sheet is seen on aggregation, crucially, however, each protein also retains a significant proportion of its native monomeric structure after aggregation. Thus, spectral analysis of each aggregated species, oligomeric, as well as fibrillar, for each protein resulted in a unique and quantitative "conformational fingerprint". This approach allowed us to provide the first differential detection of both oligomers and fibrils of the three different amyloidogenic proteins, including tau, whose aggregates have never before been interrogated using spontaneous Raman spectroscopy. Quantitative "conformational fingerprinting" by Raman spectroscopy thus demonstrates its huge potential and utility in understanding proteinopathic disease mechanisms and for providing strain-specific early diagnostic markers and targets for disease-modifying therapies.

Stereostructural Elucidation of Glucose Phosphorylation by Raman Optical Activity

Phosphorylation of glucose is the prime step in sugar metabolism and energy storage. Two key glucose phosphates are involved, that is, glucose 6-phosphate (G6P) and α-glucose 1-phosphate (αG1P). The chiral conformation of glucose, G6P, and αG1P plays an essential role in enzyme-mediated conversions. However, few techniques were able to give a direct view of the conformational changes from glucose to G6P and αG1P. Here, Raman optical activity (ROA) was used to elucidate the stereochemical evolution of glucose upon phosphorylation. ROA was found to be extremely sensitive to different phosphorylation sites. A characteristic ROA marker of (+)980 cm^-1, originated from the phosphate group symmetric stretching vibration, is observed for αG1P with phosphorylation at chiral C1, while no corresponding ROA signal for G6P with phosphorylation at achiral C6 is observed. Phosphorylation-induced gauch-gauch (gg)/gauch-trans (gt) rotamer distribution changes can be sensitively probed by the sign of the ROA band around 1460 cm^-1. A positive ROA band at 1465 cm^-1 of glucose corresponds to a higher gt ratio, while a negative band at 1455 cm^-1 of G6P suggests a dominant gg population, and the disappearance of this ROA band for αG1P indicates a nearly balanced gg/gt distribution. Meanwhile, the phosphorylation at C6 and C1 could cause dramatic reduction of the conformational flexibility of the adjacent C4-OH and C2-OH, respectively. These stereochemical changes revealed by ROA spectra offer a structural basis on the understanding of sugar phosphorylation from the perspective of chirality.

iMulti-HumPhos: a multi-label classifier for identifying human phosphorylated proteins using multiple kernel learning based support vector machines

An efficient multi-label classifier for identifying human phosphorylated proteins has been developed by introducing multiple kernel learning based support vector machines.

Rescue from tau-induced neuronal dysfunction produces insoluble tau oligomers

Aggregation of highly phosphorylated tau is a hallmark of Alzheimer’s disease and other tauopathies. Nevertheless, animal models demonstrate that tau-mediated dysfunction/toxicity may not require large tau aggregates but instead may be caused by soluble hyper-phosphorylated tau or by small tau oligomers. Challenging this widely held view, we use multiple techniques to show that insoluble tau oligomers form in conditions where tau-mediated dysfunction is rescued in vivo. This shows that tau oligomers are not necessarily always toxic. Furthermore, their formation correlates with increased tau levels, caused intriguingly, by either pharmacological or genetic inhibition of tau kinase glycogen-synthase-kinase-3beta (GSK-3β). Moreover, contrary to common belief, these tau oligomers were neither highly phosphorylated, and nor did they contain beta-pleated sheet structure. This may explain their lack of toxicity. Our study makes the novel observation that tau also forms non-toxic insoluble oligomers in vivo in addition to toxic oligomers, which have been reported by others. Whether these are inert or actively protective remains to be established. Nevertheless, this has wide implications for emerging therapeutic strategies such as those that target dissolution of tau oligomers as they may be ineffective or even counterproductive unless they act on the relevant toxic oligomeric tau species.

Protein phosphorylation detection using dual-mode field-effect devices and nanoplasmonic sensors

Phosphorylation by kinases is an important post-translational modification of proteins. It is a critical control for the regulation of vital cellular activities, and its dysregulation is implicated in several diseases. A common drug discovery approach involves, therefore, time-consuming screenings of large libraries of candidate compounds to identify novel inhibitors of protein kinases. In this work, we propose a novel method that combines localized surface plasmon resonance (LSPR) and electrolyte insulator semiconductor (EIS)-based proton detection for the rapid identification of novel protein kinase inhibitors. In particular, the selective detection of thiophosphorylated proteins by LSPR is achieved by changing their resonance properties via a pre-binding with gold nanoparticles. In parallel, the EIS field-effect structure allows the real-time electrochemical monitoring of the protein phosphorylation by detecting the release of protons associated with the kinases activity. This innovative combination of both field-effect and nanoplasmonic sensing makes the detection of protein phosphorylation more reliable and effective. As a result, the screening of protein kinase inhibitors becomes more rapid, sensitive, robust and cost-effective.

Protein phosphorylation analysis based on proton release detection: potential tools for drug discovery

Phosphorylation is the most important post-translational modification of proteins in eukaryotic cells and it is catalysed by enzymes called kinases. The balance between protein phosphorylation and dephosphorylation is critical for the regulation of physiological processes and its unbalance is the cause of several diseases. Conventional assays used to analyse the kinase activity are limited as they rely heavily on phospho-specific antibodies and radioactive tags. This makes their use impractical for high throughput drug discovery platforms. We have developed two versatile methods to detect the release of protons (H(+)) associated with the protein phosphorylation catalysed by kinases. The first approach is based on the pH-sensitive response of oxide-semiconductor interfaces and the second method detects the pH changes in phosphorylation reaction using a commercial micro-pH electrode. The proposed methods successfully detected phosphorylation of myelin basic protein by PKC-α kinase. These techniques can be readily adopted for multiplexed arrays and high throughput analysis of kinase activity, which will represent an important innovation in biomedical research and drug discovery.

Direct detection of phoxim in water by two-dimensional correlation near-infrared spectroscopy combined with partial least squares discriminant analysis

This paper has established a simple method to detect directly phoxim in water. In the light of two-dimensional correlation analysis, the band of wavenumber for near-infrared spectroscopy of the model is between 5364.8 and 7552.9 cm(-1), the rate of accuracy for partial least squares discriminant analysis to calibration set (n=149) is 100%, prediction set (n=75) is 93.3% and the overall rate of accuracy for all the samples is 97.8% under the limit of detection 1 μg ml(-1) owing to the spectra preprocessing by standard normal variate transformation and multiplicative scatter correction. It is made clear that this method (two-dimensional correlation analysis combined with partial least squares discriminant analysis) is effective to detect directly phoxim in water.

The importance of protonation in the investigation of protein phosphorylation using Raman spectroscopy and Raman optical activity

The effect of protonation on amino acid monomers and protein phosphorylation was studied by means of a combination of Raman scattering and Raman optical activity (ROA). In the past, identifying spectral variations in phosphorylated proteins arising from either the phosphate stretch or amide vibrational modes has proven to be challenging mainly due to the loss of amide and P═O band intensity in the presence of phosphate. By contrast, we have developed a novel strategy based on the careful monitoring of the sample pH and thereby modified the protonation state, such that these difficulties can be overcome and phosphate-derived vibrations are readily visualized with both Raman and ROA. Variations in pH-dependent spectral sets of phosphorylated amino acid monomers serine and threonine demonstrated that the protonation state could be determined by the intensity of the monobasic (-OPO(3)H(-)) phosphate stretch band occurring at ~1080 cm(-1) versus the dibasic (-OPO(3)(2-)) band measured at ~980 cm(-1) in both Raman and ROA. Furthermore, by adjustment of the pH of aqueous samples of the phosphoprotein α-casein and comparing this result with dephosphorylated α-casein, spectral variations in phosphate stretch bands and amide bands could be easily determined. Consequently, structural variations due to both protonation and dephosphorylation could be distinguished, demonstrating the potential of Raman and ROA for future investigations of phosphoprotein structure and interactions.

Observation of water dangling OH bonds around dissolved nonpolar groups

We report the experimental observation of water dangling OH bonds in the hydration shells around dissolved nonpolar (hydrocarbon) groups. The results are obtained by combining vibrational (Raman) spectroscopy and multivariate curve resolution (MCR), to reveal a high-frequency OH stretch peak arising from the hydration shell around nonpolar (hydrocarbon) solute groups. The frequency and width of the observed peak is similar to that of dangling OH bonds previously detected at macroscopic air-water and oil-water interfaces. The area of the observed peak is used to quantify the number of water dangling bonds around hydrocarbon chains of different length. Molecular dynamics simulation of the vibrational spectra of water molecules in the hydration shell around neopentane and benzene reveals high-frequency OH features that closely resemble the experimentally observed dangling OH vibrational bands around neopentyl alcohol and benzyl alcohol. The red-shift of approximately 50 cm(-1) induced by aromatic solutes is similar to that previously observed upon formation of a pi-H bond (in low-temperature benzene-water clusters).

Cell kinase activity assay based on surface enhanced Raman spectroscopy

Kinases control many important aspects of cell behavior, such as signal transduction, growth/differentiation, and tumorogenesis. Current methods for assessing kinase activity often require specific antibodies, and/or radioactive labeling. Here we demonstrated a novel detection method to assess kinase activity based on surface enhanced Raman spectroscopy (SERS). Raman signal was obtained after amplification by silver nanoparticles. The sensitivity of this method was comparable to fluorescence measurement of peptide concentration. When purified kinase enzyme was used, the detection limit was comparable to conventional radio-labeling method. We further demonstrated the feasibility to measure kinase activity in crude cell lysate. We suggested this SERS-based kinase activity assay could be a new tool for biomedical research and application.

Plasma-enhanced synthesis of thin fluoropolymer layers with low Raman and fluorescence backgrounds

Radio-frequency (RF) plasma enhanced chemical vapor deposition (PECVD) provides a promising way to deposit extremely hydrophobic, highly adherent nanometer- to micrometer-thick films with thermal stability, a low coefficient of friction, a low dielectric constant, and a low value of surface energy. We describe the synthesis of these fluorinated thin films using hexafluoropropene as starting material and discuss their properties. These coatings, applied to stainless steel, provide ideal substrates for Raman spectroscopy, when extremely low backgrounds are required. Raman spectroscopy measurements of a low-concentration protein film are used to demonstrate sensitivity and level of detectability.

Analysis of insulin amyloid fibrils by Raman spectroscopy

The formation of amyloid fibrils from insulin is investigated using drop-coating-deposition-Raman (DCDR) difference spectroscopy and atomic force microscopy (AFM). Fibrils formed using various co-solvents and heating cycles are found to induce the appearance of Raman difference peaks in the amide I (approximately 1675 cm(-1)), amide III (approximately 1220 cm(-1)), and peptide backbone (approximately 1010 cm(-1)), consistent with an increase in beta-sheet content. Comparisons of results obtained from fibrils in either H2O or D2O suggest that the NH/ND stretch bands (at approximately 3300 cm(-1)/ approximately 2400 cm(-1)) are also enhanced in intensity upon fibril formation. If there is any water trapped in the core of the fibrils its OH/OD Raman intensity is too small to be detected in the presence of the stronger NH/ND bands which appear in the same region. AFM is used to confirm the formation of fibrils of about 5 nm diameter (and various lengths).

Validation of the drop coating deposition Raman method for protein analysis

Drop coating deposition Raman (DCDR) spectroscopy is critically evaluated to establish the limits to which it may be used to detect changes in protein conformation, binding, and purity. Difference spectroscopy is used to evaluate the reproducibility of the DCDR spectra under various experimental conditions. The results indicate (i) the absence of thermal/photochemical laser damage induced by the Raman excitation laser under typical DCDR data collection conditions, (ii) the reproducibility of DCDR spectra from samples with different volumes or concentrations, (iii) the water content of DCDR protein deposits and associated spectral signatures, and (iv) the degree of similarity between solution Raman spectra and DCDR spectra.

Detection of amino acid and peptide phosphate protonation using Raman spectroscopy

Raman spectra of phosphorylated amino acids and peptides undergo pH-dependent changes attributed to protonation of -OPO(3)(2-) (dibasic) to -OPO(3)H(-) (monobasic). Bands at approximately 980 and 1080cm(-1) in solution Raman spectra of phosphoserine and phosphothreonine are assigned to the monobasic and dibasic phosphate groups, respectively. Calibrated Raman peak area ratio measurements, performed as a function of pH, are used to determine the corresponding pKa values of 5.6 (phosphoserine) and 5.9 (phosphothreonine). In peptides, the phosphate Raman bands are difficult to distinguish due to interference from other neighboring bands (particularly those derived from aromatic amino acid residues) as well as the relatively low solubility of peptides. Nevertheless, drop coating deposition Raman (DCDR) spectra obtained from 100-microM peptide solutions reveal pH-dependent second derivative features at approximately 980 and 1080cm(-1), which are indicative of phosphate protonation.

Identification of insulin variants using Raman spectroscopy

Drop coating deposition Raman (DCDR) spectroscopy is used to obtain high-quality normal Raman spectra from small volumes (10 microl) of dilute insulin solutions (3-400 microM) for spectral identification and chromatographic detection. The results are used to demonstrate the spectroscopic classification (identification) of three natural insulin variants-human, bovine, and porcine-that differ by between one and three amino acid residues. DCDR measurements were performed on solutions obtained from reverse phase high-performance liquid chromatography (RP-HPLC) eluent fractions, either before or after lyophilization. Classification is demonstrated using replicate DCDR measurements, followed by normalized Savitsky-Golay second derivative preprocessing and partial least squares training with either leave-one-out or batch-to-batch testing.

The Raman detection of peptide tyrosine phosphorylation

Drop-coating-deposition-Raman (DCDR) is used to detect spectral changes induced by phosphorylation of tyrosine amino acid residues in peptides. Four peptides are investigated, with sequences derived from the human protein-tyrosine kinase, p60c-src, with Y-216, Y-419, and Y-530 phosphorylation sites. Although the spectra of the four peptides are quite different, tyrosine phosphorylation is found to invariably induce the collapse of a doublet at 820-850cm(-1) and the attenuation of a peak around 1205cm(-1). Moreover, amide III band shifts suggest that tyrosine phosphorylation may promote beta sheet formation, particularly in peptides that lack phenylalanine residues. The degree of tyrosine phosphorylation in peptide mixtures is determined using DCDR combined with partial least squares multivariate calibration with a 2% root mean standard error of prediction.