Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy

Assessment of transglutaminase catalyzed cross-linking on the potential allergenicity and conformation of heterologous protein polymers

Transglutaminase (TGase)-mediated cross-linking has gained significant attention due to its potential to reduce the allergenicity of food proteins. This study investigates the effects of TGase cross-linking on allergenicity and conformational modifications in a dual-protein system comprising soy protein isolate (SPI) and β-lactoglobulin (β-LG). The results showed that TGase cross-linking effectively decreased the allergenic potential of both SPI and β-LG, with a more pronounced reduction observed in the allergenicity of soy protein in the dual-protein system. SDS-PAGE analysis revealed that the 7S and 11S subunits of soy protein were more easily cross-linked than β-LG. Secondary structure analysis indicated that TGase treatment disrupted β-sheet structures, increased the content of random coils, and enhanced protein flexibility. Ultraviolet absorption and intrinsic fluorescence analyses confirmed these structural alterations, with TGase treatment exposing additional aromatic amino acids. A reduction in free sulfhydryl groups and altered intermolecular forces further corroborated the occurrence of cross-linking. These findings suggest that TGase-mediated cross-linking effectively reduced the allergenicity of SPI and β-LG by modifying their conformations, offering potential strategies for the development of hypoallergenic dual-protein food products. PRACTICAL APPLICATION: This study has practical applications in the food industry to develop hypoallergenic food products, particularly those that combine soy and dairy proteins. By using TGase to cross-link these proteins, the allergenicity can be reduced, resulting in products that are safer for consumers with food allergies.

Selective excitation of vibrations in a single molecule

The capability to excite, probe, and manipulate vibrational modes is essential for understanding and controlling chemical reactions at the molecular level. Recent advancements in tip-enhanced Raman spectroscopies have enabled the probing of vibrational fingerprints in a single molecule with Ångström-scale spatial resolution. However, achieving controllable excitation of specific vibrational modes in individual molecules remains challenging. Here, we demonstrate the selective excitation and probing of vibrational modes in single deprotonated phthalocyanine molecules utilizing resonance Raman spectroscopy in a scanning tunneling microscope. Selective excitation is achieved by finely tuning the excitation wavelength of the laser to be resonant with the vibronic transitions between the molecular ground electronic state and the vibrational levels in the excited electronic state, resulting in the state-selective enhancement of the resonance Raman signal. Our approach contributes to setting the stage for steering chemical transformations in molecules on surfaces by selective excitation of molecular vibrations.

Raman spectroscopy coupled with chemometrics for identification of adulteration and fraud in muscle foods: a review

Muscle foods, valued for their significant nutrient content such as high-quality protein, vitamins, and minerals, are vulnerable to adulteration and fraud, stemming from dishonest vendor practices and insufficient market oversight. Traditional analytical methods, often limited to laboratory-scale., may not effectively detect adulteration and fraud in complex applications. Raman spectroscopy (RS), encompassing techniques like Surface-enhanced RS (SERS), Dispersive RS (DRS), Fourier transform RS (FTRS), Resonance Raman spectroscopy (RRS), and Spatially offset RS (SORS) combined with chemometrics, presents a potent approach for both qualitative and quantitative analysis of muscle food adulteration. This technology is characterized by its efficiency, rapidity, and noninvasive nature. This paper systematically summarizes and comparatively analyzes RS technology principles, emphasizing its practicality and efficacy in detecting muscle food adulteration and fraud when combined with chemometrics. The paper also discusses the existing challenges and future prospects in this field, providing essential insights for reviews and scientific research in related fields.

Digestion-Resistant Linear Epitopes as Dominant Contributors to Strong Allergenicity of Tropomyosin in Antarctic Krill (Euphausia superba)

Although tropomyosin has been identified as a major allergen in Antarctic krill, the digestive fate of Antarctic krill tropomyosin and its relationship with allergenicity are unknown. In this study, Antarctic krill tropomyosin was administered to BALB/c mice via both gavage and intraperitoneal injection to explore its sensitizing and eliciting capacity, and its digestion products were analyzed for structural changes and digestion-resistant linear epitopes. Mice gavaged with tropomyosin exhibited lower levels of specific IgE and IgG1, mast cell degranulation, vascular permeability, and anaphylaxis symptoms than those in the intraperitoneal injection group. This may be due to the destruction of macromolecular aggregates, loose expansion of the tertiary structure, complete disappearance of α-helix, and significant changes in molecular force upon the digestion of tropomyosin. Nevertheless, the intragastric administration of Antarctic krill tropomyosin still triggered strong allergic reactions, which was attributed to the existence of seven digestion-resistant linear epitopes (Glu26-His44, Thr111-Arg125, Glu157-Glu164, Glu177-Gly186, Val209-Ile225, Arg244-Arg255, and Val261-Ile270).

Tracking intracellular nuclear targeted-chemotherapy of chidamide-loaded Prussian blue nanocarriers by SERS mapping

The novel histone deacetylase drug chidamide (CHI) has been proven to regulate gene expression associated with oncogenesis via epigenetic mechanisms. However, huge side effects such as non-targeting, poor intracellular accumulation and low nuclear entry efficiency severely restrict its therapeutic efficacy. Dual-targeted nanodrug delivery systems have been proposed as the solution. Herein, we developed a CHI-loaded drug delivery nanosystem based on Prussian blue (PB) nanocarrier, which combines surface-enhanced Raman scattering (SERS) tracking function with cancer cell/nuclear-targeted chemotherapy capability. With the property of background-free SERS mapping, PB nanocarriers can serve as tracking agents to localize intracellular CHI. The incorporation of targeted molecules specifically enhances the cancer cell/nuclear internalization and chemotherapeutic effects of CHI-loaded PB nanocarriers. In vitro cytotoxicity assay clearly shows that the constructed CHI-loaded PB nanocarriers have significant inhibitory on Jurkat cell proliferation. Furthermore, SERS spectral analysis of Jurkat cells incubated with the CHI-loaded PB nanocarriers reveals obvious features of cellular apoptosis: DNA skeleton fragmentation, chromatin depolymerization, histone acetylation, and nucleosome conformation change. Importantly, this CHI-loaded PB nanocarrier will provide a new insight for lymphoblastic leukemia targeted chemotherapy.

The degree of doneness affected molecular changes and protein digestibility of pork

The degree of doneness has been shown to have a great impact on eating quality of meat, however, it is little known whether it affects protein digestibility of meat. In this study, we explored molecular changes and protein digestibility of pork under different degree of doneness. Pork chops were cooked in a 100°C water bath for about 26 min and a gradient decrease in doneness was obtained from outer to inner layers of samples. Compared with the raw samples, the cooked samples' active and total sulfhydryl contents, surface hydrophobicity, and turbidity increased but its solubility decreased. The inner layers with lower doneness contained higher α-helix, and fluorescence intensities of tryptophan and tyrosine residues than the outer layers with higher doneness. The pepsin and pancreatin digestibility of meat proteins in the inner layers were higher than those of the outer layers. Molecular simulation analysis showed that the most abundant protein in pork, i.e., myosin in the outer layers were more stable with an increased number of hydrogen bonds, making it difficult to be digested. These findings provided a new insight into the heterogeneity of meat nutritional quality due to the existence of doneness gradient.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

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.

Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL

Signal transduction proteins perceive external stimuli in their sensor module and regulate the biological activities of the effector module, allowing cellular adaptation in response to environmental changes. FixL is a dimeric heme protein kinase that senses the oxygen level in plant root nodules to regulate the transcription of nitrogen fixation genes via the phosphorylation of its cognate transcriptional activator. Dissociation of oxygen from the heme induces conformational changes in the protein, converting it from the inactive form for phosphorylation to the active form. However, how FixL undergoes conformational change to regulate kinase activity upon oxygen dissociation remains poorly understood. Here we report time-resolved ultraviolet resonance Raman spectra showing conformational changes for FixL from Sinorhizobium meliloti. We observed spectral changes with a time constant of about 3 μs, which were oxygen-specific. Furthermore, we found that the conformational changes in the sensor and kinase domains are coupled, enabling allosteric control of kinase activity. Our results demonstrate that concerted structural changes on the microsecond time scale serve as the regulatory switch in FixL.

Probing the Charge Transfer in a Frustrated Lewis Pair by Resonance Raman Spectroscopy and DFT Calculations

A classical Lewis adduct derives from a covalent bond between a Lewis acid and a base. When the adduct formation is precluded by means of steric hindrance the association of the respective acid-base molecular system is defined as a frustrated Lewis pair (FLP). In this work, the archetypal FLP Mes₃ P/B(C₆ F₅ )₃ was characterized for the first time by resonance Raman spectroscopy, and the results were supported by density functional theory (DFT) calculations. The charge transfer nature of the lowest energy electronic transition, from phosphine to borane, was confirmed by the selective enhancement of the Raman bands associated to the FLP chromophore at resonance condition. Herein, we demonstrate the use of resonance Raman spectroscopy as a distinguished technique to probe the weak interaction involved in FLP chemistry.

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 critical review of recent trends, and a future perspective of optical spectroscopy as PAT in biopharmaceutical downstream processing

As competition in the biopharmaceutical market gets keener due to the market entry of biosimilars, process analytical technologies (PATs) play an important role for process automation and cost reduction. This article will give a general overview and address the recent innovations and applications of spectroscopic methods as PAT tools in the downstream processing of biologics. As data analysis strategies are a crucial part of PAT, the review discusses frequently used data analysis techniques and addresses data fusion methodologies as the combination of several sensors is moving forward in the field. The last chapter will give an outlook on the application of spectroscopic methods in combination with chemometrics and model predictive control (MPC) for downstream processes. Graphical abstract.

Raman Scattering: From Structural Biology to Medical Applications

This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

UV Resonance Raman Spectroscopy as a Tool to Probe Membrane Protein Structure and Dynamics

Ultraviolet resonance Raman (UVRR) spectroscopy is a vibrational technique that reveals structures and dynamics of biological macromolecules without the use of extrinsic labels. By tuning the Raman excitation wavelength to the deep UV region (e.g., 228 nm), Raman signal from tryptophan and tyrosine residues are selectively enhanced, allowing for the study of these functionally relevant amino acids in lipid and aqueous environments. In this chapter, we present methods on the UVRR data acquisition and analysis of the tryptophan vibrational modes of a model β-barrel membrane protein, OmpA, in folded and unfolded conformations.