Beta-sheet and associated turn signatures in vibrational Raman optical activity spectra of proteins

Revisiting the conformational transition model for the pH dependence of BSA structure using photoluminescence, circular dichroism, and ellipsometric Raman spectroscopy

Changes in pH affect metabolic pathways, primarily by modulating enzyme conformations, which is why a detailed analysis of pH-driven conformational transitions is required to understand the underlying biochemistry of diseases and biological organisms. In this work, we examined the pH-driven conformational dynamics of Bovine Serum Albumin (BSA), within the framework of the Foster Model. Circular Dichroism and Raman Optical Activity showed the conversion of helical into β-rich structures in the acid and basic regions, while an opening of BSA tertiary structure was shown by the upsurging of accessibility of ANS-BSA binding sites and the increasing of random contributions at regions F and B. We could then revisit the Foster Model by introducing two additional intermediate conformational states and structural reorganization at extreme pH values. This expanded model opens up new possibilities concerning protein-molecule interactions, promising far-reaching implications for fields such as drug design and biomaterials.

Exceptionally enhanced Raman optical activity (ROA) of amyloid fibrils and their prefibrillar states

Amyloid fibrils form remarkable, multi-layered chiral supramolecular architectures. The proximity of interacting oscillators in the chiral fibril supramolecules is responsible for the unusual sensitivity of vibrational circular dichroism (VCD) for fibril formation. Surprisingly, up to now, such characteristics have not been shown for ROA, although it displays the same vibrational markers of fibrils as VCD, including the amide I band. Here, we report an exceptionally large enhancement of the ROA signal detected for mature amyloid fibrils and their prefibrillar states. Remarkably, the same ROA signal has been obtained for fibrils of homologous lysozymes and the dissimilar protein, insulin, indicating a possible common enhanced ROA spectrum, analogous to that for VCD for all amyloid fibrils investigated to date. The ROA signal is observed at earlier stages of fibril formation than VCD and provides access to a considerably broader range of vibrations. Further studies are necessary to verify the applicability of ROA for the analysis of amyloid fibrils.

Piezoresistive MXene/Silk fibroin nanocomposite hydrogel for accelerating bone regeneration by Re-establishing electrical microenvironment

The electrical microenvironment plays an important role in bone repair. However, the underlying mechanism by which electrical stimulation (ES) promotes bone regeneration remains unclear, limiting the design of bone microenvironment–specific electroactive materials. Herein, by simple co-incubation in aqueous suspensions at physiological temperatures, biocompatible regenerated silk fibroin (RSF) is found to assemble into nanofibrils with a β-sheet structure on MXene nanosheets, which has been reported to inhibit the restacking and oxidation of MXene. An electroactive hydrogel based on RSF and bioencapsulated MXene is thus prepared to promote efficient bone regeneration. This MXene/RSF hydrogel also acts as a piezoresistive pressure transducer, which can potentially be utilized to monitor the electrophysiological microenvironment. RNA sequencing is performed to explore the underlying mechanisms, which can activate Ca²⁺/CALM signaling in favor of the direct osteogenesis process. ES is found to facilitate indirect osteogenesis by promoting the polarization of M2 macrophages, as well as stimulating the neogenesis and migration of endotheliocytes. Consistent improvements in bone regeneration and angiogenesis are observed with MXene/RSF hydrogels under ES in vivo. Collectively, the MXene/RSF hydrogel provides a distinctive and promising strategy for promoting direct osteogenesis, regulating immune microenvironment and neovascularization under ES, leading to re-establish electrical microenvironment for bone regeneration.

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MXene nanosheets could direct the selective growth of silk nanofibrils.

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Prepared MXene/RSF hydrogel exhibited good conductivity and sensing ability.

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The electroactive hydrogel could promote osteogenic differentiation of BMSCs by activating the Ca²⁺/CALM signaling pathway.

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The conductive system created an osteoblast–macrophage–endotheliocyte virtuous circle for bone microenvironment.

Vibrational Optical Activity Study of Four Antibiotic (Lipo)glycopeptides: Vancomycin, Oritavancin, Dalbavancin, and Teicoplanin

The antibiotic glycopeptide class, of which vancomycin is the original compound, has received due attention over the past few decades in search of antibiotics to overcome resistances developed by bacteria. Crucial for the understanding and further development of glycopeptides that possess desired antibacterial effects is the determination of their conformational behavior, as this sheds light on the mechanism of action of the compound. Among others, vibrational optical activity (VOA) techniques (vibrational circular dichroism and Raman optical activity) can be deployed for this, but the question remains to what extent these spectroscopic techniques can provide information concerning the molecular class under investigation. This contribution takes the last hurdle in the search for the capabilities of the VOA techniques in the conformational analysis of the antibiotic glycopeptide class by extending research that was previously conducted for vancomycin toward its three derivatives: oritavancin, dalbavancin, and teicoplanin. The principal information that can be drawn from VOA spectra is the conformation of the rigid cyclic parts of the glycopeptides and the aromatic rings that are part hereof. The addition or removal of carbohydrates does not induce noticeable VOA spectral responses, preventing the determination of the conformation they adopt.

Tackling Stereochemistry in Drug Molecules with Vibrational Optical Activity

Chirality plays a crucial role in drug discovery and development. As a result, a significant number of commercially available drugs are structurally dissymmetric and enantiomerically pure. The determination of the exact 3D structure of drug candidates is, consequently, of paramount importance for the pharmaceutical industry in different stages of the discovery pipeline. Traditionally the assignment of the absolute configuration of druggable molecules has been carried out by means of X-ray crystallography. Nevertheless, not all molecules are suitable for single-crystal growing. Additionally, valuable information about the conformational dynamics of drug candidates is lost in the solid state. As an alternative, vibrational optical activity (VOA) methods have emerged as powerful tools to assess the stereochemistry of drug molecules directly in solution. These methods include vibrational circular dichroism (VCD) and Raman optical activity (ROA). Despite their potential, VCD and ROA are still unheard of to many organic and medicinal chemists. Therefore, the present review aims at highlighting the recent use of VOA methods for the assignment of the absolute configuration of chiral small-molecule drugs, as well as for the structural analysis of biologics of pharmaceutical interest. A brief introduction on VCD and ROA theory and the best experimental practices for using these methods will be provided along with selected representative examples over the last five years. As VCD and ROA are commonly used in combination with quantum calculations, some guidelines will also be presented for the reliable simulation of chiroptical spectra. Special attention will be paid to the complementarity of VCD and ROA to unambiguously assess the stereochemical properties of pharmaceuticals.

A study on the response of FRET based DNA aptasensors in intracellular environment

This paper presents a study of the response of FRET based DNA aptasensors in the intracellular environment. Herein, we extend previous studies of aptasensors functioning in the extracellular environment to detection of antigens in the intracellular environment. An essential step in this research is the use of a novel means of achieving the endocytosis of aptasensors. Specifically, it is demonstrated that functioning aptasensors are successfully endocytosed by functionalizing the aptasensors with endocytosis—inducing DSS peptides.

An Overview of Current Methods to Confirm Protein-Protein Interactions

BACKGROUND

The research field of protein-protein interactions is interdisciplinary and specialized field that spans all aspects of biology, physics and chemistry. Therefore, in order to discuss the protein-protein interaction in detail and rigorously, it is desirable to integrate knowledge and methods of many related fields including boundary areas such as biochemistry, biophysics and physical chemistry in addition to biology, physics and chemistry.

OBJECTIVE

The purpose of this review is to overview current methods to confirm protein-protein interactions. Furthermore, I discuss future prospects of methodology based on current status.

RESULTS

It is often necessary to integrate, combine and validate multiple results from various methods to understand protein-protein interactions in detail.

CONCLUSION

It might be desirable for the addition of tags, labeling, and immobilization to solid phases to be unnecessary, and to obtain information on affinity, kinetics, and structure via the analytical method for protein-protein interactions. Therefore, I argue that novel methods based on principles that have already been sufficiently studied in physics or chemistry, but insufficiently applied to the life sciences, should be established to further develop the study of protein-protein interactions.

Establishing the link between fibril formation and Raman optical activity spectra of insulin

Molecular dynamics and density functional simulations are used to explain changes in Raman optical activity accompanying the formation of insulin fibrils.

Protein Interactions Investigated by the Raman Spectroscopy for Biosensor Applications

Interaction and surface binding characteristics of staphylococcal protein A (SpA) and an anti-Escherichia coli immunoglobulin G (IgG) were studied using the Raman spectroscopy. The tyrosine amino acid residues present in the α-helix structure of SpA were found to be involved in interaction with IgG. In bulk interaction condition the native structure of proteins was almost preserved where interaction-related changes were observed in the overall secondary structure (α-helix) of SpA. In the adsorbed state, the protein structure was largely modified, which allowed the identification of tyrosine amino acids involved in SpA and IgG interaction. This study constitutes a direct Raman spectroscopic investigation of SpA and IgG (receptor-antibody) interaction mechanism in the goal of a future biosensor application for detection of pathogenic microorganisms.

Solution structure and dynamics of biomolecules from Raman optical activity

Raman optical activity (ROA) measures vibrational optical activity by means of a small difference in the intensity of Raman scattering from chiral molecules in right and left circularly polarized incident laser light. The ROA spectra of a wide range of biomolecules in aqueous solution can now be measured routinely. Because of its sensitivity to the chiral elements of biomolecular structure, ROA provides new information about solution structure and dynamics complementary to that supplied by conventional spectroscopic techniques. This article provides a brief introduction to the theory and practice of ROA spectroscopy followed by a review of recent ROA results on polypeptides, proteins, carbohydrates, nucleic acids and viruses which illustrate how new insight into current problems of structure, folding and function may be obtained from ROA studies.

New insight into the pH-dependent conformational changes in bovine beta-lactoglobulin from Raman optical activity

We have studied the conformation of beta-lactoglobulin in aqueous solution at room temperature over the pH range approximately 2.0-9.0 using vibrational Raman optical activity (ROA). The ROA spectra clearly show that the basic up and down beta-barrel core is preserved over the entire pH range, in agreement with other studies. However, from the shift of a sharp positive ROA band at approximately 1268 to approximately 1294 cm(-1) on going from pH values below that of the Tanford transition, which is centered at pH approximately 7.5, to values above, the Tanford transition appears to be associated with changes in the local conformations of residues in loop sequences possibly corresponding to a migration into the alpha-helical region of the Ramachandran surface from a nearby region. These changes may be related to those detected in X-ray crystal structures which revealed that the Tanford transition is associated with conformational changes in loops which form a doorway to the interior of the protein. The results illustrate how the ability of ROA to detect loop and turn structure separately from secondary structure is useful for studying conformational plasticity in proteins.

Vibrational optical activity of oligopeptides

Vibrational optical activity (VOA) is a relatively new spectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations.

Vibrational Raman optical activity of glycoproteins

This paper reports the first vibrational Raman optical activity (ROA) spectrum of a glycoprotein. The sample, orosomucoid (alpha 1-acid glycoprotein), shows ROA bands characteristic of a high beta-sheet content together with new bands which could be specific for the carbohydrate and its association with the protein. Our results suggest that ROA spectra of intact glycoproteins may contain information about both protein and carbohydrate conformation and the mutual influence on each other's stability and conformation.