Proteins can convert to beta-sheet in single crystals

Flavones Suppress Aggregation and Amyloid Fibril Formation of Human Lysozyme under Macromolecular Crowding Conditions

The crowded milieu of a biological cell significantly impacts protein aggregation and interactions. Understanding the effects of macromolecular crowding on the aggregation and fibrillation of amyloidogenic proteins is crucial for the treatment of many amyloid-related disorders. Most in vitro studies of protein amyloid formation and its inhibition by small molecules are conducted in dilute buffers, which do not mimic the complexity of the cellular environment. In this study, we used PEGs to simulate macromolecular crowding and examined the inhibitory effects of flavones DHF, baicalein, and luteolin on human lysozyme (HuL) aggregation at pH 2. Naturally occurring flavones have been effective inhibitors of amyloid formation in some proteins. Our findings indicate that while flavones inhibit HuL aggregation and fibrillation in dilute buffer solutions, complete inhibition is observed with a combination of flavones and PEGs, as shown by ThT fluorescence, light scattering, TEM, and AFM studies. The species formed in the presence of PEG 8000 and flavones were less hydrophobic, less toxic, and α-helix-rich compared to control samples, which were hydrophobic and β-sheet-rich, as demonstrated by ANS hydrophobicity, MTT assay, and CD spectroscopy. Fluorescence titration studies of flavones with HuL showed a significant increase in binding constant values under crowding conditions. These findings highlight the importance of macromolecular crowding in modulating protein aggregation and amyloid inhibition. Further studies using disease-causing mutants of HuL and other amyloidogenic proteins are needed to explore the role of macromolecular crowding in small-molecule-mediated modulation and inhibition of protein aggregation and amyloid formation.

Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates

Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.

pH-Responsive Protein Conformation Transistor

Analogous to electronic transistors, transistor-like responsive materials undergo sharp structural transitions in response to a very narrow range of microenvironment signals. This kind of material is typically limited to synthetic polymer-derived nanoscale assembly or disassembly and has profound implications for modern high-tech applications. Herein, we evolve this system from synthetic polymers to biopolymers and extend the corresponding assembly scale from the nanoscale to meso/macro-scale. We develop unique protein nanocrystals with core-shell structures through a two-step nucleation process. The protein nanocrystals exhibit exceptional transistor-like pH-responsive mesoscale assembly through the formation of inter-particle β-sheet linkers. This allows ultrasensitive cross-linking behavior, such as self-coacervation at a water/water interface, ultrafast gelation in seconds, and ultrasensitive swelling for detection of basic vapors at extremely low concentrations. This breakthrough has great promise for broader applications such as drug encapsulation and delivery, biosensing, cytomimetic materials, and microfluidic chemistry.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Label-free SERS for rapid identification of interleukin 6 based on intrinsic SERS fingerprint of antibody‑gold nanoparticles conjugate

A label-free surface-enhanced Raman scattering (SERS) was designed for sensitive detection of interleukin-6 (IL-6). The sensing element composed of anti-IL-6 antibodies adsorbed on the surface of spherical gold nanoparticles (AuNPs) as SERS-active surface. The principle of detection was probing antibody conformational changes using its intrinsic SERS fingerprint after binding to IL-6. Comparison of SERS spectra of antibody before and after binding to IL-6 showed that secondary structure of antibody does not change upon binding to IL-6. Vibrational information from disulfide bonds ν(SS) in antibody structure indicated some changes of geometry around SS bridges as a consequence of the immunocomplex formation. Transmission electron microscopy (TEM) and UV-Vis spectroscopy were used to confirm AuNPs conjugation with antibody as well as IL-6 binding to antibody on the surface of AuNPs. The SERS-based immunoassay showed a wide linear range (2.0-1000 pg mL-1) and a high sensitivity with a limit of detection (LOD) as low as 0.91 pg mL-1 (0.04 pM) without using any extrinsic Raman label. UV-Vis spectroscopy was employed as a conventional method for IL-6 detection based on observation of any change in the position of localized surface plasmon resonance (LSPR) band of AuNPs-antibody conjugates with LOD of 10 ng mL-1.

Non-invasive identification of combined salinity stress and stalk rot disease caused by Colletotrichum graminicola in maize using Raman spectroscopy

Food security is an emerging problem that is faced by our civilization. There are millions of people around the world suffering from various kinds of malnutrition. The number of people that starve will only increase considering the continuous growth of the world's population. The problem of food security can be addressed by timely detection and identification biotic and abiotic stresses in plants that drastically reduce the crop yield. A growing body of evidence suggests that Raman spectroscopy (RS), an emerging analytical technique, can be used for the confirmatory and non-invasive diagnostics of plant stresses. However, it remains unclear whether RS can efficiently disentangle biotic and abiotic stresses, as well as detect both of them simultaneously in plants. In this work, we modeled a stalk rot disease in corn by inoculating the plant stalks with Colletotrichum graminicola. In parallel, we subjected plants to salt stress, as well as challenging plants with both stalk rot disease and salinity stress simultaneously. After the stresses were introduced, Raman spectra were collected from the stalks to reveal stress-specific changes in the plant biochemistry. We found that RS was able to differentiate between stalk rot disease and salinity stresses with 100% accuracy, as well as predict presence of both of those stresses in plants on early and late stages. These results demonstrate that RS is a robust and reliable approach that can be used for confirmatory, non-destructive and label-free diagnostics of biotic and abiotic stresses in plants.

Raman spectroscopy detects chemical differences between potato tubers produced under normal and heat stress growing conditions

Potato is the most consumed vegetable worldwide. Potato tubers contain water, starch, proteins, minerals, and vitamins. The amounts of these chemicals depend on the cultivar and growing location. When potatoes are exposed to high temperatures during the growing period, tuber yield and quality are detrimentally affected; however, there is limited knowledge about the influence of high temperatures on tuber chemical composition. With temperatures rising around the globe, the reaction of potato cultivars to high temperatures is increasingly important, and heat-induced changes, including changes in the chemical composition of tubers, should be considered. The Texas A&M University Potato Breeding Program has been selecting potato clones under high-temperature conditions for many years. Several released cultivars are considered heat-tolerant based on high marketable yields and low internal and external tuber defects. In this study, we used Raman spectroscopy (RS), an analytical tool, to determine whether heat stress causes changes in the chemical composition of tubers of ten potato cultivars. RS is a non-invasive method that requires less time and labor than conventional chemical analysis. We found drastic changes in the intensities of vibrational bands that originate from carbohydrates in the spectra acquired from tubers of heat-stressed plants compared to tubers produced by potato plants grown under normal conditions. These results demonstrate that RS could be used as a replacement or complement to conventional chemical analysis to inspect the effect of heat stress on tuber chemical composition.

Raman Spectroscopy and Improved Inception Network for Determination of FHB-Infected Wheat Kernels

Detection of infected kernels is important for Fusarium head blight (FHB) prevention and product quality assurance in wheat. In this study, Raman spectroscopy (RS) and deep learning networks were used for the determination of FHB-infected wheat kernels. First, the RS spectra of healthy, mild, and severe infection kernels were measured and spectral changes and band attribution were analyzed. Then, the Inception network was improved by residual and channel attention modules to develop the recognition models of FHB infection. The Inception–attention network produced the best determination with accuracies in training set, validation set, and prediction set of 97.13%, 91.49%, and 93.62%, among all models. The average feature map of the channel clarified the important information in feature extraction, itself required to clarify the decision-making strategy. Overall, RS and the Inception–attention network provide a noninvasive, rapid, and accurate determination of FHB-infected wheat kernels and are expected to be applied to other pathogens or diseases in various crops.

Investigating Lysosomal Autophagy via Surface-Enhanced Raman Scattering Spectroscopy

Autophagy plays a critical role in many vitally important physiological and pathological processes, such as the removal of damaged and aged organelles and redundant proteins. Although autophagy is mainly a protective process for cells, it can also cause cell death. In this study, we employed in situ and ex situ surface-enhanced Raman scattering (SERS) spectroscopies to obtain chemical information of lysosomes of HepG2 cells. Results reveal that the SERS profiles of the isolated lysosomes are different from the in situ spectra, indicating that lysosomes lie in different microenvironments in these two cases. We further investigated the molecular changes of isolated lysosomes according to the autophagy induced by starvation via ex situ SERS. During autophagy, the conformation of proteins and the structures of lipids have been affected, and autophagy-related molecular evidence is given for the first time in the living lysosomes. We expect that this study will provide a reference for understanding the cell autophagy mechanism.

Raman-Based Diagnostics of Stalk Rot Disease of Maize Caused by Colletotrichum graminicola

Stalk rot caused by Colletotrichum graminicola is a disease of worldwide importance. Stalk rot is difficult to detect at the early stages of infection because the fungus colonizes the tissues inside the maize stem. Current diagnostic methods are time-consuming, laborious, and destructive to the stem tissue. We utilized Raman spectroscopy to follow the development of stalk rot in three different maize genotypes grown either in the field or the greenhouse. We then used the acquired spectra to calibrate statistical models to differentiate amongst the different disease timepoints and the genotypes themselves. This non-invasive spectroscopic method enabled high-accuracy identification of stalk rot based on both stalk and leaf spectra. We additionally found that leaf spectra were favorable for identifying maize by genotype. Finally, we identified Raman bands that showed correlation with the sizes of stalk rot-associated lesions in the stems. We demonstrated that Raman spectroscopy is a viable tool for detection of stalk rot disease, as well as potent for the differentiation of maize genotypes.

Non-invasive identification of potato varieties and prediction of the origin of tuber cultivation using spatially offset Raman spectroscopy

High starch content, simplicity of cultivation, and high productivity make potatoes (Solanum tuberosum) a staple in the diet of people around the world. On average, potatoes are composed of 83% water and 12% carbohydrates, and the remaining 4% includes proteins, vitamins, and other trace elements. These proportions vary depending on the type of potato and location where they were cultivated. At the same time, the chemical composition determines the nutritional value of potato tubers and can be proved using various wet chemistry and spectroscopic methods. For instance, gravity measurements, as well as several different colorimetric assays, can be used to investigate the starch content. However, these approaches are indirect, often destructive, and time- and labor-consuming. This study reports on the use of Raman spectroscopy (RS) for completely non-invasive and non-destructive assessment of nutrient content of potato tubers. We also show that RS can be used to identify nine different potato varieties, as well as determine the origin of their cultivation. The portable nature of Raman-based identification of potato offers the possibility to perform such analysis directly upon potato harvesting to enable quick quality evaluation. Graphical abstract.

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.

Raman observation of a molecular signaling pathway of apoptotic cells induced by photothermal therapy

Plasmonic nanoparticle (NP)-mediated photothermal therapy (PPTT) has been explored as a minimally invasive approach to cancer therapy and has progressed from concept to the early stage of clinical trials. Better understanding of the cellular and molecular response to PPTT is crucial for improvement of therapy efficacy and advancement of clinical application. However, the molecular mechanism underlying PPTT-induced apoptosis is still unclear and under dispute. In this work, we used nuclear-targeting Au nanostars (Au NSs) as both a photothermal agent to specifically induce apoptosis in cancer cells and as a surface enhanced Raman spectroscopy (SERS) probe to monitor the time-dependent SERS spectra of MCF-7 cells which are undergoing apoptosis. Through SERS spectra and their synchronous and asynchronous SERS correlation maps, the occurrence and dynamics of a cascade of molecular events have been investigated, and a molecular signaling pathway of PPTT-induced apoptosis, including release of cytochrome c, protein degradation, and DNA fragmentation, was revealed, which was also demonstrated by metabolomics, agarose gel electrophoresis, and western blot analysis, respectively. These results indicated that PPTT-induced apoptosis undergoes an intrinsic mitochondria-mediated apoptosis pathway. Combined with western blot results, this intrinsic mitochondria-mediated apoptosis pathway was further demonstrated to be initiated by a BH3-only protein, BID. This work is beneficial for not only improving the fundamental understanding of the molecular mechanism of apoptosis induced by PPTT but also for guiding the modulation of PPTT to drive forward its clinical application.

Rapid, quantitative determination of aggregation and particle formation for antibody drug conjugate therapeutics with label-free Raman spectroscopy

Lot release and stability testing of biologics are essential parts of the quality control strategy for ensuring therapeutic material dosed to patients is safe and efficacious, and consistent with previous clinical and toxicological experience. Characterization of protein aggregation is of particular significance, as aggregates may lose the intrinsic pharmaceutical properties as well as engage with the immune system instigating undesirable downstream immunogenicity. While important, real-time identification and quantification of subvisible particles in the monoclonal antibody (mAb) drug products remains inaccessible with existing techniques due to limitations in measurement time, sensitivity or experimental conditions. Here, owing to its exquisite molecular specificity, non-perturbative nature and lack of sample preparation requirements, we propose label-free Raman spectroscopy in conjunction with multivariate analysis as a solution to this unmet need. By leveraging subtle, but consistent, differences in vibrational modes of the biologics, we have developed a support vector machine-based regression model that provides fast, accurate prediction for a wide range of protein aggregations. Moreover, in blinded experiments, the model shows the ability to precisely differentiate between aggregation levels in mAb like product samples pre- and post-isothermal incubation, where an increase in aggregate levels was experimentally determined. In addition to offering fresh insights into mAb like product-specific aggregation mechanisms that can improve engineering of new protein therapeutics, our results highlight the potential of Raman spectroscopy as an in-line analytical tool for monitoring protein particle formation.

Noninvasive and Nondestructive Detection of Cowpea Bruchid within Cowpea Seeds with a Hand-Held Raman Spectrometer

Insect damage to crops is a serious issue, in particular when the pest dwells within its host. The cowpea bruchid ( Callosobruchus maculatus) is an herbivore of legumes including beans and peas. The bruchid lays its eggs on the seeds themselves; after hatching, the larvae burrow into and develop inside the seed, complicating detection and treatment. Left unchecked, two insects could destroy up to 50% of 1 ton of harvest cowpea ( Vigna unguiculata) after several months of storage. In this study, we investigated the possibility of using a hand-held Raman spectrometer to detect the pest during its development within intact cowpeas. Our results show that Raman spectroscopy can detect chemical signatures of bruchid larvae as well as their excrements inside the intact seeds. Additionally, using chemometric methods, we distinguished between healthy and infested seeds as well as among seeds hosting developmentally early or late-stage larvae with high accuracy. This study demonstrates Raman spectroscopy's efficacy in not only detection of pathogens and pests present on the surface of plant leaves and the grain but also inside the seeds. This Raman-based method may prove useful as a rapid means of screening crops for internal pests.

Developing Biopolymer Mesocrystals by Crystallization of Secondary Structures

Particle-based mesocrystals have been known for over 10 years; however, examples of biopolymer mesocrystals are rather scarce. The synthesis of particle precursors of biopolymers, the identification of particle-mediated crystallization processes, and thus the synthesis of mesocrystals of biopolymers are challenging. Here, we summarize the existing examples of biopolymer crystallization based on self-assembly of the secondary structures, which could induce the formation of biopolymer mesocrystals. As basic building units, simple secondary structures such as β-sheets or α-helixes could provide a useful tool for the design of biopolymer mesocrystals.

Nucleus and Mitochondria Targeting Theranostic Plasmonic Surface-Enhanced Raman Spectroscopy Nanoprobes as a Means for Revealing Molecular Stress Response Differences in Hyperthermia Cell Death between Cancerous and Normal Cells

Metallic plasmonic nanoparticles have been intensively exploited as theranostic nanoprobes for plasmonic photothermal therapy (PPT) and surface-enhanced Raman spectroscopy (SERS) applications. But the underlying molecular mechanisms associated with PPT-induced apoptosis between cancerous and normal cells have remained largely unknown or disputed. In this study, we designed an organelle-targeting theranostic plasmonic SERS nanoprobe (CDs-Ag/Au NS) composed of porous Ag/Au nanoshell (p-Ag/Au NSs) and carbon dots (CDs) for nucleus and mitochondria targeted PPT of cells. The differences in molecular stress response in the PPT-induced hyperthermia cell death between cancerous HeLa and normal L929 and H8 cells have been revealed by site-specific single-cell SERS detection. The contents of tryptophan (Trp), phenylalanine (Phe), and tyrosine (Tyr) in HeLa cells were found more evidently increased than L929 and H8 cells during the PPT-induced cell-death process. And from the mitochondria point of view, we found that the PPT-induced cell apoptosis for HeLa cells mainly stems from (or is regulated through) cellular thermal stress-responsive proteins, while for L929 and H8 cells it seems more related to DNA. Understanding molecular stress response difference of the PPT-induced cell apoptosis between cancerous and normal cells is helpful for diagnosis and treatment of cancer, and the method will open an avenue for single-cell studies.

Raman spectroscopy in pharmaceutical research and industry

In the fast-developing fields of pharmaceutical research and industry, the implementation of Raman spectroscopy and related technologies has been very well received due to the combination of chemical selectivity and the option for non-invasive analysis of samples. This chapter explores established and potential applications of Raman spectroscopy, confocal Raman microscopy and related techniques from the early stages of drug development research up to the implementation of these techniques in process analytical technology (PAT) concepts for large-scale production in the pharmaceutical industry. Within this chapter, the implementation of Raman spectroscopy in the process of selection and optimisation of active pharmaceutical ingredients (APIs) and investigation of the interaction with excipients is described. Going beyond the scope of early drug development, the reader is introduced to the use of Raman techniques for the characterization of complex drug delivery systems, highlighting the technical requirements and describing the analysis of qualitative and quantitative composition as well as spatial component distribution within these pharmaceutical systems. Further, the reader is introduced to the application of Raman techniques for performance testing of drug delivery systems addressing drug release kinetics and interactions with biological systems ranging from single cells up to complex tissues. In the last part of this chapter, the advantages and recent developments of integrating Raman technologies into PAT processes for solid drug delivery systems and biologically derived pharmaceutics are discussed, demonstrating the impact of the technique on current quality control standards in industrial production and providing good prospects for future developments in the field of quality control at the terminal part of the supply chain and various other fields like individualized medicine.

On the way from the active drug molecule (API) in the research laboratory to the marketed medicine in the pharmacy, therapeutic efficacy of the active molecule and safety of the final medicine for the patient are of utmost importance. For each step, strict regulatory requirements apply which demand for suitable analytical techniques to acquire robust data to understand and control design, manufacturing and industrial large-scale production of medicines. In this context, Raman spectroscopy has come to the fore due to the combination of chemical selectivity and the option for non-invasive analysis of samples. Following the technical advancements in Raman equipment and analysis software, Raman spectroscopy and microscopy proofed to be valuable methods with versatile applications in pharmaceutical research and industry, starting from the analysis of single drug molecules as well as complex multi-component formulations up to automatized quality control during industrial production.

Investigating the autophagy pathway in silver@gold core-shell nanoparticles-treated cells using surface-enhanced Raman scattering

Previous studies have shown that nanoparticles can induce autophagy, and the main approach for investigating autophagy induced by nanoparticles is via traditional methods such as TEM and biochemical assay. These methods measurements suffer from the disadvantages of complicated experimental processes, cell destruction, as well as lack of characterization of individual stages of the autophagy pathway. Surface-enhanced Raman scattering (SERS) has been extensively used in biological applications. With the combination of SERS and chemometric methods, such as principal component analysis-linear discriminant analysis (PCA-LDA), identification and distribution mapping of endosomes and lysosomes in the endocytosis of Au nanoparticles has been achieved by segregating the spectra from complex SERS data sets in the previous study. In this study, silver@gold core-shell nanoparticles (Ag@Au NPs) were synthesized by reduction of gold ions on the surface of the silver nanoparticles, and the autophagy induced by Ag@Au NPs was studied with Ag@Au NPs serving both as an autophagy inducer and as a high-performance SERS substrate. Pro-survival autophagy induced by Ag@Au NPs was proved by the western blot assay, flow cytometry and fluorescent staining. Furthermore, the autophagy pathway in Ag@Au NPs-treated cells was first elucidated by SERS combined with a modified reference-based PCA-LDA methodology. This study provides a feasible way of using SERS to elucidate the autophagy pathway induced by nanoparticles.

Rapidly responsive silk fibroin hydrogels as an artificial matrix for the programmed tumor cells death

Timely and spatially-regulated injectable hydrogels, able to suppress growing tumors in response to conformational transitions of proteins, are of great interest in cancer research and treatment. Herein, we report rapidly responsive silk fibroin (SF) hydrogels formed by a horseradish peroxidase (HRP) crosslinking reaction at physiological conditions, and demonstrate their use as an artificial biomimetic three-dimensional (3D) matrix. The proposed SF hydrogels presented a viscoelastic nature of injectable hydrogels and spontaneous conformational changes from random coil to β-sheet conformation under physiological conditions. A human neuronal glioblastoma (U251) cell line was used for screening cell encapsulation and in vitro evaluation within the SF hydrogels. The transparent random coil SF hydrogels promoted cell viability and proliferation up to 10 days of culturing, while the crystalline SF hydrogels converted into β-sheet structure induced the formation of TUNEL-positive apoptotic cells. Therefore, this work provides a powerful tool for the investigation of the microenvironment on the programed tumor cells death, by using rapidly responsive SF hydrogels as 3D in vitro tumor models.

Structural Insight of Amyloidogenic Intermediates of Human Insulin

Engaging Raman spectroscopy as a primary tool, we investigated the early events of insulin fibrilization and determined the structural content present in oligomer and protofibrils that are formed as intermediates in the fibril formation pathway. Insulin oligomer, as obtained upon incubation of zinc-free insulin at 60 °C, was mostly spherical in shape, with a diameter of 3-5 nm. Longer incubation produced "necklace"-like beaded protofibrillar assembly species. These intermediates eventually transformed into 5-8 nm thick fibers with smooth surface texture. A broad amide I band in the Raman spectrum of insulin monomer appeared at 1659 cm^-1, with a shoulder band at 1676 cm^-1. This signature suggested the presence of major helical and extended secondary structure of the protein backbone. In the oligomeric state, the protein maintained its helical imprint (∼50%) and no substantial increment of the compact cross-β-sheet structure was observed. A nonamide helix signature band at 940 cm^-1 was present in the oligomeric state, and it was weakened in the fibrillar structure. The 1-anilino-8-naphthalene-sulfonate binding study strongly suggested that a collapse in the tertiary structure, not the major secondary structural realignment, was the dominant factor in the formation of oligomers. In the fibrillar state, the contents of helical and disordered secondary structures decreased significantly and the β-sheet amount increased to ∼62%. The narrow amide I Raman band at 1674 cm^-1 in the fibrillar state connoted the formation of vibrationally restricted highly organized β-sheet structure with quaternary realignment into steric-zipped species.

Envisaging the Structural Elevation in the Early Event of Oligomerization of Disordered Amyloid β Peptide

In Alzheimer's disease (AD), amyloid β (Aβ) protein plays a detrimental role in neuronal injury and death. Recent in vitro and in vivo studies suggest that soluble oligomers of the Aβ peptide are neurotoxic. Structural properties of the oligomeric assembly, however, are largely unknown. Our present investigation established that the 40-residue-long Aβ peptide (Aβ40) became more helical, ordered, and compact in the oligomeric state, and both the helical and β-sheet components were found to increase significantly in the early event of oligomerization. The band-selective two-dimensional NMR analysis suggested that majority of the residues from sequence 12 to 22 gained a higher-ordered secondary structure in the oligomeric condition. The presence of a significant amount of helical conformation was confirmed by Raman bands at 1650 and 1336 cm^-1. Other residues remained mostly in the extended polyproline II (PPII) and less compact β-conformation space. In the event of maturation of the oligomers into an amyloid fiber, both the helical content and the PPII-like structural components declined and ∼72% residues attained a compact β-sheet structure. Interestingly, however, some residues remained in the collagen triple helix/extended 2.5₁-helix conformation as evidenced by the amide III Raman signature band at 1272 cm^-1. Molecular dynamics analysis using an optimized potential for liquid simulation force field with the peptide monomer indicated that some of the residues may have preferences for helical conformation and this possibly contributed in the event of oligomer formation, which eventually became a β-sheet-rich amyloid fiber.

Plasmon-enhanced Raman spectroscopic metrics for in situ quantitative and dynamic assays of cell apoptosis and necrosis

Plasmon-enhanced Raman spectroscopic metrics were developed for in situ quantitative and dynamic assays of viable, apoptotic and necrotic cells.

Apoptosis and necrosis are distinct cell death processes related to many cellular pathways. In situ, quantitatively and dynamically monitoring such processes may provide vitally important information for cell studies. However, such a method still remains elusive, even though current immunochemical methodologies have developed extremely valuable tools. Herein, we demonstrate Raman spectroscopic metrics for validating and quantifying apoptotic and necrotic cells based on their distinct molecular vibrational fingerprints. It not only allows us to quantify apoptotic and necrotic cell populations in situ in adherent cell samples, but also to be capable of continuously monitoring the dynamical processes of apoptosis and necrosis at the same time in one sample. This method provides comparable results with the “gold standard” of flow cytometry, moreover, with several incomparable advantages. Our work offers a powerful new tool for cell apoptosis and necrosis assays and is expected to become a benchmark technology in biological and medical studies.

Surface-Enhanced Raman Scattering to Evaluate Nanomaterial Cytotoxicity on Living Cells

The increasing number of reports about false positive or negative results from conventional cytotoxicity assays of nanomaterials (NMs) suggests that more reliable NM toxicity assessment methods should be developed. Here, we report a novel approach for nanotoxicity evaluation based on surface-enhanced Raman spectroscopy (SERS). Three model NMs were tested on two model cell lines and the results were validated by WST-1 cytotoxicity assay and annexin V-FITC/propidium iodide (PI) staining as apoptosis-necrosis assay. The localization of nanoparticles (NPs) in the cells and the cellular conditions upon NP incubation were visualized by transmission electron microscopy (TEM) and enhanced dark-field (EDF) microscopy. SERS revealed a broader view on the consequences of cell-NM interactions compared to the conventional cytotoxicity assays where only one aspect of toxicity can be measured by one assay type. The results suggest that SERS can significantly contribute to the cytotoxicity evaluation bypassing NM or assay component-related complications with less effort.

Morphological Versatility in the Self-Assembly of Val-Ala and Ala-Val Dipeptides

Since the discovery of dipeptide self-assembly, diphenylalanine (Phe-Phe)-based dipeptides have been widely investigated in a variety of fields. Although various supramolecular Phe-Phe-based structures including tubes, vesicles, fibrils, sheets, necklaces, flakes, ribbons, and wires have been demonstrated by manipulating the external physical or chemical conditions applied, studies of the morphological diversity of dipeptides other than Phe-Phe are still required to understand both how these small molecules respond to external conditions such as the type of solvent and how the peptide sequence affects self-assembly and the corresponding molecular structures. In this work, we investigated the self-assembly of valine-alanine (Val-Ala) and alanine-valine (Ala-Val) dipeptides by varying the solvent medium. It was observed that Val-Ala dipeptide molecules may generate unique self-assembly-based morphologies in response to the solvent medium used. Interestingly, when Ala-Val dipeptides were utilized as a peptide source instead of Val-Ala, we observed distinct differences in the final dipeptide structures. We believe that such manipulation may not only provide us with a better understanding of the fundamentals of the dipeptide self-assembly process but also may enable us to generate novel peptide-based materials for various applications.

Heating-induced transition of Potyvirus Potato Virus A coat protein into β-structure

In our previous communication, we have reported that virions of plant Potyvirus Potato Virus A (PVA) have a peculiar structure characterized by high content of disordered regions in intravirus coat protein (CP). In this report, we describe unusual properties of the PVA CP. With the help of a number of physicochemical methods, we have observed that the PVA CP just released from the virions by heating at 60-70 °C undergoes association into oligomers and transition to β- (and even cross-β-) conformation. Transition to β-structure on heating has been recently reported for a number of viral and non-viral proteins. The PVA CP isolated by LiCl method was also transformed into cross-β-structure on heating to 60 °C. Using the algorithms for protein aggregation prediction, we found that the aggregation-prone segments should be located in the central region of a PVA CP molecule. Possibly this transition mimics some functions of PVA CP in the virus life cycle in infected plants.

Time-resolved Raman and polyacrylamide gel electrophoresis observations of nucleotide incorporation and misincorporation in RNA within a bacterial RNA polymerase crystal

The bacterial RNA polymerase (RNAP) elongation complex (EC) is highly stable and is able to extend an RNA chain for thousands of nucleotides. Understanding the processive mechanism of nucleotide addition requires detailed structural and temporal data for the EC reaction. Here, a time-resolved Raman spectroscopic analysis is combined with polyacrylamide gel electrophoresis (PAGE) to monitor nucleotide addition in single crystals of the Thermus thermophilus EC (TthEC) RNAP. When the cognate base GTP, labeled with (13)C and (15)N (*GTP), is soaked into crystals of the TthEC, changes in the Raman spectra show evidence of nucleotide incorporation and product formation. The major change is the reduction of *GTP's triphosphate intensity. Nucleotide incorporation is confirmed by PAGE assays. Both Raman and PAGE methods have a time resolution of minutes. There is also Raman spectroscopic evidence of a second population of *GTP in the crystal that does not become covalently linked to the nascent RNA chain. When this population is removed by "soaking out" (placing the crystal in a solution that contains no NTP), there are no perturbations to the Raman difference spectra, indicating that conformational changes are not detected in the EC. In contrast, the misincorporation of the noncognate base, (13)C- and (15)N-labeled UTP (*UTP), gives rise to large spectroscopic changes. As in the GTP experiment, reduction of the triphosphate relative intensity in the Raman soak-in data shows that the incorporation reaction occurs during the first few minutes of our instrumental dead time. This is also confirmed by PAGE analysis. Whereas PAGE data show *GTP converts 100% of the nascent RNA 14mer to 15mer, the noncognate *UTP converts only ∼50%. During *UTP soak-in, there is a slow, reversible formation of an α-helical amide I band in the Raman difference spectra peaking at 40 min. Similar to *GTP soak-in, *UTP soak-in shows Raman spectoscopic evidence of a second noncovalently bound *UTP population in the crystal. Moreover, the second population has a marked effect on the complex's conformational states because removing it by "soaking-out" unreacted *UTP causes large changes in protein and nucleic acid Raman marker bands in the time range of 10-100 min. The conformational changes observed for noncognate *UTP may indicate that the enzyme is preparing for proofreading to excise the misincorporated base. This idea is supported by the PAGE results for *UTP soak-out that show endonuclease activity is occurring.

Observing real-time molecular event dynamics of apoptosis in living cancer cells using nuclear-targeted plasmonically enhanced Raman nanoprobes

Apoptosis is a biological process that plays important roles in embryogenesis, aging, and various diseases. During the process of apoptosis, cells undergo a series of morphological and molecular events such as blebbing, cell shrinkage, proteolysis, and nuclear DNA fragmentation. Investigating these events on a molecular level is crucial for gaining a more complete understanding of the intricate mechanism of apoptosis; however, the simultaneous direct observation of morphological and molecular events in real-time on a single living cell scale still remains a challenge. Herein, we directly monitored morphological and molecular events during cellular apoptosis in real-time after the treatment of an apoptosis-inducing agent, by utilizing our previously described plasmonically enhanced Rayleigh/Raman spectroscopic technique. Spectroscopic analysis of the DNA/protein composition around the cell nucleus revealed the occurrence and dynamics of three apoptotic molecular events: protein denaturation, proteolysis, and DNA fragmentation. The molecular event dynamics were used to create a temporal profile of apoptotic events in single cells. It is found that the sequence of events occurring in the apoptotic process induced by hydrogen peroxide addition is protein denaturation through disulfide bond breakage as well as DNA fragmentation, followed in time by protein unraveling with hydrophobic amino acid exposure, and finally protein degradation. These results demonstrate the potential of using this time-dependent plasmonically enhanced vibrational imaging technique to study the detailed mechanism of other apoptosis molecular pathways induced by different agents (e.g., anticancer drugs). A note is given in the conclusion discussing the expected large difference between the SERS spectrum of biological molecules in solution and that observed in live cells which are enhanced by the plasmonic field of the aggregated nanoparticles.

Monitoring guanidinium-induced structural changes in ribonuclease proteins using Raman spectroscopy and 2D correlation analysis

Assessing the stability of proteins by comparing their unfolding profiles is a very important characterization and quality control step for any biopharmaceutical, and this is usually measured by fluorescence spectroscopy. In this paper we propose Raman spectroscopy as a rapid, noninvasive alternative analytical method and we shall show this has enhanced sensitivity and can therefore reveal very subtle protein conformational changes that are not observed with fluorescence measurements. Raman spectroscopy is a powerful nondestructive method that has a strong history of applications in protein characterization. In this work we describe how Raman microscopy can be used as a fast and reliable method of tracking protein unfolding in the presence of a chemical denaturant. We have compared Raman spectroscopic data to the equivalent samples analyzed using fluorescence spectroscopy in order to validate the Raman approach. Calculations from both Raman and fluorescence unfolding curves of [D]50 values and Gibbs free energy correlate well with each other and more importantly agree with the values found in the literature for these proteins. In addition, 2D correlation analysis has been performed on both Raman and fluorescence data sets in order to allow further comparisons of the unfolding behavior indicated by each method. As many biopharmaceuticals are glycosylated in order to be functional, we compare the unfolding profiles of a protein (RNase A) and a glycoprotein (RNase B) as measured by Raman spectroscopy and discuss the implications that glycosylation has on the stability of the protein.

A new nanotechnology technique for determining drug efficacy using targeted plasmonically enhanced single cell imaging spectroscopy

Recently, we described a new technique, targeted plasmonically enhanced single cell imaging spectroscopy (T-PESCIS), which exploits the plasmonic properties of gold nanoparticles, e.g. gold nanospheres, to simultaneously obtain enhanced intracellular Raman molecular spectra and enhanced Rayleigh cell scattering images throughout the entire span of a single cell cycle. In the present work, we demonstrate the use of T-PESCIS in evaluating the relative efficacy and dynamics of two popular chemotherapy drugs on human oral squamous carcinoma (HSC-3) cells. T-PESCIS revealed three plasmonically enhanced Raman scattering vibration bands, 500, 1000, and 1585 cm(-1), associated with the cellular death dynamics. Detailed analysis indicated that the decrease in the 500 cm(-1) band did not correlate well with drug efficacy but could indicate death initiation. The time it takes for the relative intensity of either the 1000 or 1585 cm(-1) band ("SERS death" bands) to appear and increase to its maximum value after the injection of a known concentration of the drug can be related to the drug's efficacy. The inverse ratio, termed cell death enhancement factor, of these characteristic death times when using either band, especially the spectrally sharp band at 1000 cm(-1), gave the correct drug efficacy ratio as determined by the commonly used XTT cell viability assay method. These results strongly suggest the potential future use of this technique in determining the efficacy, dynamics, and molecular mechanisms of various drugs against different diseases.

Confocal microscopy on the beamline: novel three-dimensional imaging and sample positioning

Confocal microscopy, a technique that has been extensively applied in cellular biological studies, may also be applied to the visualization and three-dimensional imaging of protein crystals at high resolution on synchrotron beamlines. Protein crystal samples are examined using a commercially available confocal microscope adapted for cryogenic use. A preliminary test using a custom confocal design adapted for beamline use is also presented. The confocal optics configuration is compatible with nonlinear imaging techniques such as two-photon excited fluorescence imaging and second harmonic generation. The possibilities of this method are explored using two modes: fluorescence and reflection confocal. In fluorescence mode, small amounts of dye are introduced into the crystal through soaking or growth conditions. Under such conditions, protein crystals are easily resolved from salts and amorphous precipitates, which do not generally take up dye. Reflection mode, which does not require dye, still exhibits greater resolution and sensitivity to surface detail than conventional wide-field microscopy as a result of the confocal optics configuration. The inherent three-dimensional nature of the method means that on-axis sample views (along the direction of the X-ray beam) can be reconstructed from an off-axis configuration, simplifying the beamline setup and providing uniquely detailed views of cryogenically cooled crystals.

Monitoring the glycosylation status of proteins using Raman spectroscopy

Protein-based biopharmaceuticals are becoming increasingly widely used as therapeutic agents, and the characterization of these biopharmaceuticals poses a significant analytical challenge. In particular, monitoring posttranslational modifications (PTMs), such as glycosylation, is an important aspect of this characterization because these glycans can strongly affect the stability, immunogenicity, and pharmacokinetics of these biotherapeutic drugs. Raman spectroscopy is a powerful tool, with many emerging applications in the bioprocessing arena. Although the technique has a relatively rich history in protein science, only recently has Raman spectroscopy been investigated for assessing posttranslational modifications, including phosphorylation, acetylation, trimethylation, and ubiquitination. In this investigation, we develop for the first time Raman spectroscopy combined with multivariate data analyses, including principal components analysis and partial least-squares regression, for the determination of the glycosylation status of proteins and quantifying the relative concentrations of the native ribonuclease (RNase) A protein and RNase B glycoprotein within mixtures.

Kinetic crystallography by Raman microscopy

Raman spectra, obtained using a Raman microscope, offer a unique and incisive approach to follow interactions and reactions inside a single crystal under soak-in or soak-out conditions. The utility of this approach derives from the finding that the Raman spectra from single macromolecular crystals, under normal (non-resonance) conditions, are extremely stable, with a low "light background," and provide ideal platforms for Raman difference spectroscopy. In turn, this allows the interrogation of sub-molecular changes in very large and complex macromolecular environments. There is often great synergy with X-ray crystallography, with the Raman spectroscopist providing crystallography colleagues with the best soak-in conditions to generate a targeted intermediate for flash freezing and X-ray analysis. On the other hand, X-ray structures at points along a reaction pathway provide invaluable benchmarks for interpreting the Raman data from populations seen by Raman to be changing in real-time. These principles will be illustrated by two reactions: the first involves a complex, branching reaction pathway underlying the inhibition of β-lactamases by clinically important pharmaceutical compounds, where different combinations of drug and enzyme function in different regions of the pathway. The second shows how temporal data can be derived for several events in the initiation step of RNA synthesis-more specifically, when one GTP molecule is joined to one ATP molecule to form a G∙A dimer in the active site of a 115,000 Dalton crystalline RNA polymerase. Finally, we will summarize the extension of Raman microscopy to nucleic acid crystals and the information that has been obtained for RNA-based enzymes. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Raman-assisted crystallography of biomolecules at the synchrotron: instrumentation, methods and applications

Raman spectroscopy is a powerful technique that, in recent years, has been successfully coupled to X-ray crystallography for the analysis of biological macromolecular systems. The complementarity between both techniques is illustrated at multiple stages, including sample preparation, data collection and structural interpretation with a mechanistic perspective. The current state of instrumentation is described, focusing on synchrotron based setups. Present and future applications of Raman microspectrophotometry are reviewed with reference to recent examples dealing with metallo-, photosensitive-, and redox-proteins. The added value of Raman microspectrophotometry to assess X-radiation damage is discussed, and its applicability to investigate crystalline DNA molecules is also emphasized. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Different intermediate populations formed by tazobactam, sulbactam, and clavulanate reacting with SHV-1 beta-lactamases: Raman crystallographic evidence

Tazobactam, sulbactam, and clavulanic acid are the only beta-lactamase inhibitors in clinical use. Comparative inhibitory activities of clavulanic acid, sulbactam, and tazobactam against clinically important beta-lactamases conclude that tazobactam is superior to both clavulanic acid and sulbactam. Thus far, the majority of explanations for this phenomenon have relied on kinetic studies, which report differences in the ligands' apparent dissociation constants and number of turnovers before inactivation. Due their innate limitations, these investigations do not examine the identity of intermediates on the reaction pathway and relate them to the efficacy of the inhibitors. In the present study, the reactions between the three inhibitors and SHV-1 beta-lactamase have been examined in single crystals using a Raman microscope. The results show that tazobactam forms a predominant population of trans-enamine, a chemically inert species, with SHV-1, while clavulanate and sulbactam form a mixture of trans-enamine and two labile species, the cis-enamine and imine. The same reactions are then reexamined using a deacylation-deficient variant, SHV E166A, that has been used to trap acyl-enzyme intermediates for X-ray crystallographic analysis. Our Raman data show that significant differences exist between the wild-type and SHV E166A acyl-enzyme populations. Namely, compared to SHV-1, sulbactam shows significantly smaller populations of cis-enamine and imine in the E166A variant, while clavulanate exists almost exclusively as trans-enamine in the E166A active site. Using clavulanate as an example, we also show that Raman crystallography can provide novel information on the presence of multiple conformers or tautomers for intermediates within a complex reaction pathway. These insights caution against the interpretation of experimental data obtained with deacylation-deficient beta-lactamases to make mechanistic conclusions about inhibitors within the enzyme.

Raman spectroscopy of protein pharmaceuticals

Recent advances in optical and spectroscopic technologies have enabled a plethora of Raman spectrometers that are suitable for studies of protein pharmaceuticals. Highly sensitive Raman spectrometers have overcome the handicap of the fundamentally weak Raman effect that hampered their applications to protein pharmaceuticals in the past. These Raman spectrometers can now routinely measure protein therapeutics at the low concentration of 1 mg/mL, which is on par with other spectroscopic methods such as CD, fluorescence and FTIR spectroscopies. In this article, various Raman techniques that can be used for protein pharmaceutical studies are reviewed. Novel Raman marker of proteins discovered from fundamental studies of protein complexes are examined along with established Raman spectra and structure correlations. Examples of Raman spectroscopic studies of protein pharmaceuticals are demonstrated. Future applications of Raman spectroscopy to protein pharmaceuticals are discussed.

RAMAN CRYSTALLOGRAPHY AND OTHER BIOCHEMICAL APPLICATIONS OF RAMAN MICROSCOPY

Recent studies using a Raman microscope have shown that single protein crystals provide an ideal platform to undertake Raman difference spectroscopic analyses under nonresonance conditions. This approach, termed Raman crystallography, provides a means of characterizing chemical events within the crystal such as ligand binding and enzyme reactions. In many cases Raman crystallography goes hand in hand with X-ray crystallographic studies because the Raman results can inform the X-ray crystallographer about the status of chemical events in the crystal prior to flash freezing and X-ray analysis. In turn, the combined data from the Raman and X-ray analyses are highly synergistic and offer novel perspectives on structure and dynamics in enzyme active sites. In a related area, protein misfolding, Raman microscopy can provide detailed insights into the chemistry of the amyloid plaques associated with Alzheimer's disease and into the intermediates on the alpha-synuclein protein misfolding pathway implicated in Parkinson's disease.

Microspectrophotometry for structural enzymology

For several decades, single-crystal microspectrophotometry has contributed to structural enzymology as a very useful complement to X-ray crystallography. In its most recent applications, it is the ideal tool to track chemistry as structure evolves in the course of time-resolved experiments, to identify freeze-trapped catalytic intermediates and to assess radiation-induced effects on enzyme crystals. To these goals, instruments have been developed to record optical spectra 'on-line' in the course of X-ray data collection, whereas more rigorous polarized absorption studies 'off-line' play an essential role in describing what protein function is retained in the crystalline state and correlating it with the observed structures.