Ultraviolet Resonance Raman Spectroscopic Markers for Protein Structure and Dynamics

A Visual Raman Nano-Delivery System Based on Thiophene Polymer for Microtumor Detection

A visual Raman nano-delivery system (NS) is a widely used technique for the visualization and diagnosis of tumors and various biological processes. Thiophene-based organic polymers exhibit excellent biocompatibility, making them promising candidates for development as a visual Raman NS. However, materials based on thiophene face limitations due to their absorption spectra not matching with NIR (near-infrared) excitation light, which makes it difficult to achieve enhanced Raman properties and also introduces potential fluorescence interference. In this study, we introduce a donor-acceptor (D-A)-structured thiophene-based polymer, PBDB-T. Due to the D-A molecular modulation, PBDB-T exhibits a narrow bandgap of Eg = 2.63 eV and a red-shifted absorption spectrum, with the absorption edge extending into the NIR region. Upon optimal excitation with 785 nm light, it achieves ultra-strong pre-resonant Raman enhancement while avoiding fluorescence interference. As an intrinsically sensitive visual Raman NS for in vivo imaging, the PBDB-T NS enables the diagnosis of microtumor regions with dimensions of 0.5 mm × 0.9 mm, and also successfully diagnoses deeper tumor tissues, with an in vivo circulation half-life of 14.5 h. This research unveils the potential application of PBDB-T as a NIR excited visual Raman NS for microtumor diagnosis, introducing a new platform for the advancement of "Visualized Drug Delivery Systems". Moreover, the aforementioned platform enables the development of a more diverse range of targeted visual drug delivery methods, which can be tailored to specific regions.

A review: Exploring the metabolic and structural characterisation of beta pleated amyloid fibril in human tissue using Raman spectrometry and SAXS

Amyloidosis is a deleterious condition caused by abnormal amyloid fibril build-up in living tissues. To date, 42 proteins that are linked to amyloid fibrils have been discovered. Amyloid fibril structure variation can affect the severity, progression rate, or clinical symptoms of amyloidosis. Since amyloid fibril build-up is the primary pathological basis for various neurodegenerative illnesses, characterization of these deadly proteins, particularly utilising optical techniques have been a focus. Spectroscopy techniques provide significant non-invasive platforms for the investigation of the structure and conformation of amyloid fibrils, offering a wide spectrum of analyses ranging from nanometric to micrometric size scales. Even though this area of study has been intensively explored, there still remain aspects of amyloid fibrillization that are not fully known, a matter hindering progress in treating and curing amyloidosis. This review aims to provide recent updates and comprehensive information on optical techniques for metabolic and proteomic characterization of β-pleated amyloid fibrils found in human tissue with thorough literature analysis of publications. Raman spectroscopy and SAXS are well established experimental methods for study of structural properties of biomaterials. With suitable models, they offer extended information for valid proteomic analysis under physiologically relevant conditions. This review points to evidence that despite limitations, these techniques are able to provide for the necessary output and proteomics indication in order to extrapolate the aetiology of amyloid fibrils for reliable diagnostic purposes. Our metabolic database may also contribute to elucidating the nature and function of the amyloid proteome in development and clearance of amyloid diseases.

A versatile technique for indiscriminate detection of unlabeled biomolecules via double-enhanced Raman scattering

Surface-enhanced Raman scattering is a rapid, highly sensitive and non-destructive technique, whereas, it was still limited to designing different types of enhancing substrates or using probe molecules to only identify single biomolecules. Especially, some special biomolecules have weak Raman signals in solid state, so it is a huge challenge to obtain their enhanced Raman signals in liquid. To solve the problem, a double-enhanced Raman scattering (DERS) detection platform was developed in this study based on silver nanoparticles that were prepared by using an appropriate amount of sodium borohydride and guided by calcium ions to form good "hot spots". This enabled one to successfully obtain fingerprints of various types of biomolecules under the identical experimental conditions. The addition of sodium borohydride as reducing agent could protect silver nanoparticles from oxidation, and biomolecules were adsorbed on the exposed silver surface and demonstrated their initially enhanced Raman signals. Furthermore, the "hot spots" formed by silver nanoparticles without silver oxide coating could further enhance the Raman signal of biomolecules, making the enhancement factor up to 10 [8]. To sum up, the possibility of fast identification of different species of biomolecules via DERS has wide application prospects in the fields of biomarker detection and medical diagnosis.

The Glycerol-Induced Perfusion-Kinetics of the Cat Ovaries in the Follicular and Luteal Phases of the Cycle

The method of immersion optical clearing reduces light scattering in tissues, which improves the use of optical technologies in the practice of clinicians. In this work, we studied the optical and molecular diffusion properties of cat ovarian tissues in the follicular (F-ph) and luteal (L-ph) phases under the influence of glycerol using reflectance spectroscopy in a broad wavelength range from 200 to 800 nm. It was found that the reflectance and transmittance of the ovaries are significantly lower in the range from 200 to 600 nm than for longer wavelengths from 600 to 800 nm, and the efficiency of optical clearing is much lower for the ovaries in the luteal phase compared to the follicular phase. For shorter wavelengths, the following tissue transparency windows were observed: centered at 350 nm and wide (46 ± 5) nm, centered at 500 nm and wide (25 ± 7) nm for the F-ph state and with a center of 500 nm and a width of (21 ± 6) nm for the L-ph state. Using the free diffusion model, Fick's law of molecular diffusion and the Bouguer-Beer-Lambert radiation attenuation law, the glycerol/tissue water diffusion coefficient was estimated as D = (1.9 ± 0.2)10^-6 cm²/s for ovaries at F-ph state and D = (2.4 ± 0.2)10^-6 cm²/s-in L-ph state, and the time of complete dehydration of ovarian samples, 0.8 mm thick, as 22.3 min in F-ph state and 17.7 min in L-ph state. The ability to determine the phase in which the ovaries are stated, follicular or luteal, is also important in cryopreservation, new reproductive technologies and ovarian implantation.

A Model for Inhomogeneously Broadened Raman Bands

Detailed information on the physics and chemistry of a sample can be derived from Raman band parameters. However, the Raman band observed by the detector contains artifacts from the instrument, complicating analysis of these details. To obtain Raman data that can be directly correlated to sample properties and to compare Raman spectra across instrumentation, instrumental effects must be accounted for. This is commonly performed for homogeneously broadened bands by determining the contribution of the slit function to the spectrum. However, there is currently no method for understanding instrumental effects on inhomogeneously broadened bands or a method to account for these effects when examining data and comparing data across instruments, though these analyses are commonplace. This shortfall injects an unknown error into the analyses and comparisons of inhomogeneously broadened Raman bands. This work derives a method of modeling inhomogeneous Raman bands as a continuum of homogeneous Raman bands spanning the width of the stochastic fluctuation energy well that causes inhomogeneous broadening. This model is combined with previous work to examine the effects of the slit function, intrinsic Raman band, stochastic energy well, homogeneously broadened Raman band, and slit width band parameters on the inhomogeneously broadened Raman band parameters. This model, for the first time, provides a quantitative description of the experimental parameters that effect the inhomogeneous Raman bands.

Detection of Cell-Derived Exosomes Via Surface-Enhanced Raman Scattering Using Aggregated Silver Nanoparticles

Exosomes are small extracellular vesicles that contain RNA, lipids, and proteins and can act as cellular messengers, carrying information to cells and tissues in the body. Thus, sensitive, label-free, and multiplexed analysis of exosomes may help in early diagnosis of important diseases. Here, we describe the process of pretreatment of cell-derived exosomes, preparation of surface-enhanced Raman scattering (SERS) substrates, and label-free SERS detection of exosomes using sodium borohydride aggregators. This method can enable the observation of SERS signals of exosomes that are clear and stable and have a good signal-to-noise ratio.

Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers

Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

A direct method for detecting proteins in body fluids by Surface-Enhanced Raman Spectroscopy under native conditions

Surface enhanced Raman spectroscopy (SERS) is widely used in biomolecular detection. However, maintaining the native structure of proteins while obtaining sensitive and reproducible SERS signals of unlabeled proteins remains a challenge. In this study, dichloromethane (DCM) and CaCl₂ were used to optimize the aggregation of Ag nanoparticles (AgNPs), and several proteins were analyzed comprehensively. Calcium ions removed citrate ions outside AgNPs, inducing hot spots and achieving high-sensitivity SERS signals of proteins. Furthermore, 20 random samples of 0.5 μg/mL hemoglobin were analyzed by this method. The obtained spectra showed good repeatability and a high quality. Using the peak intensity of DCM as internal parameter, the differences in peak intensities at the same position were analyzed to distinguish different proteins and evaluate changes in protein structure. Subsequently, the protein content in protein mixtures and serum was quantified and a good linear relationship between peak intensity and protein concentration was obtained. This method shows great promise in the fields of food testing and clinical diagnosis.

Strategies and Perspectives for UV Resonance Raman Applicability in Clinical Analyses of Human Sperm RNA

Developing a deeper knowledge about the impact of DNA and RNA epigenetic mutations on sperm production and fertilization performance is essential for selecting best quality samples in Assisted Reproductive Technologies (ART). Indeed, sperm RNAs adenine and guanine are likely to be methylated in low quality RNA sperm samples and their study requires the employment of techniques able to isolate high quality nucleic acids. UV resonance Raman spectroscopy represents a valuable tool that is able to monitor peculiar molecular modifications occurring predominantly in nucleic acids, being less sensitive to the presence of other biological compounds. In this work, we used an UV Resonance Raman (UVRR) setup coupled to a synchrotron radiation source tuned at 250 nm, in order to enhance sperm RNAs adenine and guanine vibrational signals, reducing also the impact of a fluorescence background typically occurring at lower energies. Despite that our protocol should be further optimized and further analyses are requested, our results support the concept that UVRR can be applied for setting inexpensive tools to be employed for semen quality assessment in ART.

UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction

Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.

Prospects of ultraviolet resonance Raman spectroscopy in supramolecular chemistry on proteins

Ultraviolet resonance Raman scattering (UVRR) has been frequently used for studying peptide and protein structure and dynamics, while applications in supramolecular chemistry are quite rare. Since UVRR offers the additional advantages of chromophore selectivity and high sensitivity compared with conventional non-resonant Raman scattering, it is ideally suited for label-free probing of relatively small artificial/supramolecular ligands exhibiting electronic resonances in the UV. In this perspective article, we first summarize results of UVRR spectroscopy in supramolecular chemistry in the context of peptide/protein recognition. We focus on selected artificial ligands which were rationally designed as selective carboxylate binders (guanidiniocarbonyl pyrrole, GCP, and guanidiniocarbonyl indole, GCI) and selective lysine binder (molecular tweezer, CLR01), respectively, via a combination of non-covalent interactions involving electrostatics, hydrogen bonding, and hydrophobic effects/van der Waals forces. Current limitations of applying UVRR as a universally applicable method for label-free and site-specific probing of molecular recognition between supramolecular ligands and proteins are highlighted. We then propose solutions to overcome these limitations for transforming UVRR spectroscopy into a generic tool in supramolecular chemistry on proteins, with an emphasis on mono- and multivalent GCP- and GCI-based ligands. Finally, we outline specific cases of supramolecular ligands such as molecular tweezers where alternative approaches such as laser-based mid-IR spectroscopy are required since UVRR can intrinsically not provide the required molecular information.

Determining the stages of cellular differentiation using deep ultraviolet resonance Raman spectroscopy

Cellular differentiation is a fundamental process in which one cell type changes into one or more specialized cell types. Cellular differentiation starts at the beginning of embryonic development when a simple zygote begins to transform into a complex multicellular organism composed of various cell and tissue types. This process continues into adulthood when adult stem cells differentiate into more specialized cells for normal growth, regeneration, repair, and cellular turnover. Any abnormalities associated with this fundamental process of cellular differentiation are linked to life-threatening conditions, including degenerative diseases and cancers. Detection of undifferentiated and different stages of differentiated cells can be used for disease diagnosis but is often challenging due to the laborious procedures, expensive tools, and specialized technical skills which are required. Here, a novel approach, called deep ultraviolet resonance Raman spectroscopy, is used to study various stages of cellular differentiation using a well-known myoblast cell line as a model system. These cells proliferate in the growth medium and spontaneously differentiate in differentiation medium into myocytes and later into myotubes. The cellular and molecular characteristics of these cells mimic very well actual muscle tissue in vivo. We have found that undifferentiated myoblast cells and myoblast cells differentiated at three different stages are able to be easily separated using deep ultraviolet resonance Raman spectroscopy in combination with chemometric techniques. Our study has a great potential to study cellular differentiation during normal development as well as to detect abnormal cellular differentiation in human pathological conditions in future studies.

Analysis of Chemisorbed Tribo-Film for Ceramic-on-Ceramic Hip Joint Prostheses by Raman Spectroscopy

To understand the possible lubricant mechanism in ceramic-on-ceramic hip joint prostheses, biochemical reactions of the synovial fluid and the corresponding frictional coefficients were studied. The experiments were performed in a hip joint simulator using the ball-on-cup configuration with balls and cups made from two types of ceramics, BIOLOX^®forte and BIOLOX^®delta. Different lubricants, namely albumin, γ-globulin, hyaluronic acid and three model synovial fluids, were studied in the experiments and Raman spectroscopy was used to analyze the biochemical responses of these lubricants at the interface. BIOLOX^®delta surface was found less reactive to proteins and model fluid lubricants. In contrast, BIOLOX^®forte ball surface has shown chemisorption with both proteins, hyaluronic acid and model fluids imitating total joint replacement and osteoarthritic joint. There was no direct correlation between the measured frictional coefficient and the observed chemical reactions. In summary, the study reveals chemistry of lubricant film formation on ceramic hip implant surfaces with various model synovial fluids and their components.

Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis

Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions. Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation. Molecular dynamics simulation results on the basis of the CHARMM36 force field showed that the α-helix LM7-2 bent around two or three residues near the middle of the peptide, stayed in a helix-hinge-helix conformation for a short period of time, and then returned to a helical conformation. High-resolution computational vibrational techniques were applied on the LM7-2 system when it has α-helical and helix-hinge-helix conformations to understand how this structural change affects its inherent vibrations. These studies concentrated on the calculation of frequencies that correspond to backbone amide bands I, II, and III: vibrational modes that are sensitive to changes in the secondary structure of peptides and proteins. To that end, Fourier transforms were applied to thermal fluctuations in C-N-H angles, C-N bond lengths, and C═O bond lengths of each amide group. In addition, instantaneous all-atom normal mode analysis was applied to monitor and detect the characteristic amide bands of each amide group within LM7-2 during the MD simulation. Computational vibrational results indicate that shapes and frequencies of amide bands II and especially III were altered only for amide groups near the hinge. These methods provide high-resolution vibrational information that can complement spectroscopic vibrational studies. They assist in interpreting spectra of similar systems and suggest a marker for the presence of the helix-hinge-helix motif. Moreover, radial distribution functions indicated an increase in the probability of hydrogen bonding between water and a hydrogen atom connected to nitrogen (HN) in such a hinge. The probability of intramolecular hydrogen bond formation between HN and an amide group oxygen atom within LM7-2 was lower around the hinge. No correlation has been found between the presence of a hinge and hydrogen bonds between amide group oxygen atoms and the hydrogen atoms of water molecules. This result suggests a mechanism for hinge formation wherein hydrogen bonds to oxygen atoms of water replace intramolecular hydrogen bonds as the peptide backbone folds.

A peroxidase coordinating to Zn (II) preventing heme bleaching and resistant to the interference of H2 O2

Dehaloperoxidase (DHP) catalyzes detoxifying halophenols. It is a heme-containing enzyme using H₂ O₂ as the oxidant. Heme bleaching from the active site is of great concern. In addition, the interference of DHP by H₂ O₂ leads to the inactivation of the enzyme. To solve these two problems, DHP is coordinated to Zn (II) in PBS buffer to form a biomineralized composite (DHP&Zn-CP). DHP&Zn-CP was characterized by measuring SEM and confocal images, as well as energy dispersive X-ray spectrometry mapping. Fluorescence spectra demonstrated that DHP&Zn-CP can prevent heme bleaching. Two-dimensional FTIR spectra were measured, dynamically providing insight into the structural change of DHP along the coordination process. Raman spectra were performed to analyze the structural change. The optical spectra confirmed that the forming of DHP&Zn-CP had a little effect on the structures of DHP. For the dehalogenation of 2,4,6-trichlorophenol, DHP&Zn-CP can tolerate the presence of H₂ O₂ and is resistant to the interference by H₂ O₂ . The catalytic efficiency of DHP&Zn-CP is much higher than that of free DHP.

Far-Off Resonance: Multiwavelength Raman Spectroscopy Probing Amide Bands of Amyloid-β-(37-42) Peptide

Several neurodegenerative diseases, like Alzheimer's and Parkinson's are linked with protein aggregation into amyloid fibrils. Conformational changes of native protein into the β-sheet structure are associated with a significant change in the vibrational spectrum. This is especially true for amide bands which are inherently sensitive to the secondary structure of a protein. Raman amide bands are greatly intensified under resonance conditions, in the UV spectral range, allowing for the selective probing of the peptide backbone. In this work, we examine parallel β-sheet forming GGVVIA, the C-terminus segment of amyloid-β peptide, using UV-Vis, FTIR, and multiwavelength Raman spectroscopy. We find that amide bands are enhanced far from the expected UV range, i.e., at 442 nm. A reasonable two-fold relative intensity increase is observed for amide II mode (normalized according to the δCH2/δCH3 vibration) while comparing 442 and 633 nm excitations; an increase in relative intensity of other amide bands was also visible. The observed relative intensification of amide II, amide S, and amide III modes in the Raman spectrum recorded at 442 nm comparing with longer wavelength (633/785/830 nm) excited spectra allows unambiguous identification of amide bands in the complex Raman spectra of peptides and proteins containing the β-sheet structure.

Order, Disorder, and Reorder State of Lysozyme: Aggregation Mechanism by Raman Spectroscopy

Lysozyme, like many other well-folded globular proteins, under stressful conditions produces nanoscale oligomer assembly and amyloid-like fibrillar aggregates. With engaging Raman microscopy, we made a critical structural analysis of oligomer and other assembly structures of lysozyme obtained from hen egg white and provided a quantitative estimation of a protein secondary structure in different states of its fibrillation. A strong amide I Raman band at 1660 cm^-1 and a N-Cα-C stretching band at ∼930 cm^-1 clearly indicated the presence of a substantial amount of α-helical folds of the protein in its oligomeric assembly state. In addition, analysis of the amide III region and Raman difference spectra suggested an ample presence of a PPII-like secondary structure in these oligomers without causing major loss of α-helical folds, which is found in the case of monomeric samples. Circular dichroism study also revealed the presence of typical α-helical folds in the oligomeric state. Nonetheless, most of the Raman bands associated with aromatic residues and disulfide (-S-S-) linkages broadened in the oligomeric state and indicated a collapse in the tertiary structure. In the fibrillar state of assembly, the amide I band became much sharper and enriched with the β-sheet secondary structure. Also, the disulfide bond vibration in matured fibrils became much weaker compared to monomer and oligomers and thus confirmed certain loss/cleavage of this bond during fibrillation. The Raman band of tryptophan and tyrosine residues indicated that some of these residues experienced a greater hydrophobic microenvironment in the fibrillar state than the protein in the oligomeric state of the assembly structure.

Moving tissue spectral window to the deep-ultraviolet via optical clearing

The optical immersion clearing technique has been successfully applied through the last 30 years in the visible to near infrared spectral range, and has proven to be a promising method to promote the application of optical technologies in clinical practice. To investigate its potential in the ultraviolet range, collimated transmittance spectra from 200 to 1000 nm were measured from colorectal muscle samples under treatment with glycerol-water solutions. The treatments created two new optical windows with transmittance efficiency peaks at 230 and 300 nm, with magnitude increasing with glycerol concentration in the treating solution. Such discovery opens the opportunity to develop clinical procedures to perform diagnosis or treatments in the ultraviolet.

Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent

Expanded polyglutamine (polyQ) tracts in proteins, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D₂Q₁₅K₂ (Q15) and D₂Q₂₀K₂ (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D₂Q₁₀K₂ (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that is thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.

UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide

Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D₂Q₂₀K₂ (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.

Challenges in application of Raman spectroscopy to biology and materials

Raman spectroscopy has become an essential tool for chemists, physicists, biologists and materials scientists. In this article, we present the challenges in unravelling the molecule-specific Raman spectral signatures of different biomolecules like proteins, nucleic acids, lipids and carbohydrates based on the review of our work and the current trends in these areas. We also show how Raman spectroscopy can be used to probe the secondary and tertiary structural changes occurring during thermal denaturation of protein and lysozyme as well as more complex biological systems like bacteria. Complex biological systems like tissues, cells, blood serum etc. are also made up of such biomolecules. Using mice liver and blood serum, it is shown that different tissues yield their unique signature Raman spectra, owing to a difference in the relative composition of the biomolecules. Additionally, recent progress in Raman spectroscopy for diagnosing a multitude of diseases ranging from cancer to infection is also presented. The second part of this article focuses on applications of Raman spectroscopy to materials. As a first example, Raman spectroscopy of a melt cast explosives formulation was carried out to monitor the changes in the peaks which indicates the potential of this technique for remote process monitoring. The second example presents various modern methods of Raman spectroscopy such as spatially offset Raman spectroscopy (SORS), reflection, transmission and universal multiple angle Raman spectroscopy (UMARS) to study layered materials. Studies on chemicals/layered materials hidden in non-metallic containers using the above variants are presented. Using suitable examples, it is shown how a specific excitation or collection geometry can yield different information about the location of materials. Additionally, it is shown that UMARS imaging can also be used as an effective tool to obtain layer specific information of materials located at depths beyond a few centimeters.

This paper reviews various facets of Raman spectroscopy. This encompasses biomolecule fingerprinting and conformational analysis, discrimination of healthy vs. diseased states, depth-specific information of materials and 3D Raman imaging.