Effect of Aggregated Lysozyme on Fluorescence Properties of Rose Bengal.

Protein aggregates cause abnormal states and trigger various diseases, including neurodegenerative disorders. This study examined whether the xanthene dye derivative Rose Bengal could track a series of conformational changes in protein aggregates. Using lysozyme as a model protein, aggregated proteins were prepared by heating under acidic conditions. The absorption spectra, steady-state fluorescence spectra, fluorescence quantum yield, fluorescence lifetime, and phosphorescence lifetime of a solution containing Rose Bengal in the presence of aggregated lysozyme were measured to identify their spectroscopic characteristics. The absorption spectrum of Rose Bengal changed significantly during the formation of agglomerates in heated lysozyme. Additionally, the fluorescence intensity decreased during the initial stages of the aggregation process with an increase in heating time, followed by an increase in intensity along with a red-shift of the peak wavelength. The decrease in quantum yield with a fixed fluorescence lifetime supported the formation of a nonfluorescent ground-state complex between Rose Bengal and the aggregated lysozyme. Based on the characteristic changes in absorption and fluorescence properties observed during the aggregation process, Rose Bengal is considered an excellent indicator for the sensitive discernment of aggregated proteins.

Polymorphism of Amyloid Fibrils Induced by Catalytic Seeding: A Vibrational Circular Dichroism Study.

Amyloidal protein fibrils occur in many biological events, but their formation and structural variability are understood rather poorly. We systematically explore fibril polymorphism for polyglutamic acid (PGA), insulin and hen egg white lysozyme. The fibrils were grown in the presence of "seeds", that is fibrils of the same or different protein. The seeds in concentrations higher than about 5 % of the total protein amount fully determined the structure of the final fibrils. Fibril structure was monitored by vibrational circular dichroism (VCD) spectroscopy and other techniques. The VCD shapes significantly differ for different fibril samples. Infrared (IR) and VCD spectra of PGA were also simulated using density functional theory (DFT) and a periodic model. The simulation provides excellent basis for data interpretation and reveals that the spectral shapes and signs depend both on fibril length and twist. The understanding of fibril formation and interactions may facilitate medical treatment of protein misfolding diseases in the future.

Dynamically Re-Organized Collagen Fiber Bundles Transmit Mechanical Signals and Induce Strongly Correlated Cell Migration and Self-Organization.

Correlated cell migration in fibrous extracellular matrix (ECM) is important in many biological processes. During migration, cells can remodel the ECM, leading to the formation of mesoscale structures such as fiber bundles. However, how such mesoscale structures regulate correlated single-cells migration remains to be elucidated. Here, using a quasi-3D in vitro model, we investigate how collagen fiber bundles are dynamically re-organized and guide cell migration. By combining laser ablation technique with 3D tracking and active-particle simulations, we definitively show that only the re-organized fiber bundles that carry significant tensile forces can guide strongly correlated cell migration, providing for the first time a direct experimental evidence supporting that matrix-transmitted long-range forces can regulate cell migration and self-organization. This force regulation mechanism can provide new insights for studies on cellular dynamics, fabrication or selection of biomedical materials in tissue repairing, and many other biomedical applications.

Naphthoquinone-Dopamine Hybrids Inhibit α-Synuclein Aggregation, Disrupt Preformed Fibrils, and Attenuate Aggregate-Induced Toxicity.

Accumulation and aggregation of the intrinsically disordered protein α-synuclein (α-Syn) into amyloid fibrils are hallmarks of a series of heterogeneous neurodegenerative disorders, known as synucleinopathies and most notably Parkinson's disease (PD). The crucial role of α-Syn aggregation in PD makes it an attractive target for the development of disease-modifying therapeutics that would inhibit α-Syn aggregation or disrupt its preformed fibrillar assemblies. To this end, we have designed and synthesized two naphthoquinone-dopamine-based hybrid small molecules, NQDA and Cl-NQDA, and demonstrated their ability to inhibit in vitro amyloid formation by α-Syn using ThT assay, CD, TEM, and Congo red birefringence. Moreover, these hybrid molecules efficiently disassembled preformed fibrils of α-Syn into nontoxic species, as evident from LUV leakage assay. NQDA and Cl-NQDA were found to have low cytotoxicity and they attenuated the toxicity induced by α-Syn towards SH-SY5Y neuroblastoma cells. NQDA was found to efficiently cross an in vitro human blood-brain barrier model. These naphthoquinone-dopamine based derivatives can be an attractive scaffold for therapeutic design towards PD.

Tracking Extracellular Matrix Remodeling in Lungs Induced by Breast Cancer Metastasis. Fourier Transform Infrared Spectroscopic Studies.

This work focused on a detailed assessment of lung tissue affected by metastasis of breast cancer. We used large-area chemical scanning implemented in Fourier transform infrared (FTIR) spectroscopic imaging supported with classical histological and morphological characterization. For the first time, we differentiated and defined biochemical changes due to metastasis observed in the lung parenchyma, atelectasis, fibrous, and muscle cells, as well as bronchi ciliate cells, in a qualitative and semi-quantitative manner based on spectral features. The results suggested that systematic extracellular matrix remodeling with the progress of the metastasis process evoked a decrease in the fraction of the total protein in atelectasis, fibrous, and muscle cells, as well as an increase of fibrillar proteins in the parenchyma. We also detected alterations in the secondary conformations of proteins in parenchyma and atelectasis and changes in the level of hydroxyproline residues and carbohydrate moieties in the parenchyma. The results indicate the usability of FTIR spectroscopy as a tool for the detection of extracellular matrix remodeling, thereby enabling the prediction of pre-metastatic niche formation.

On the Binding of Congo Red to Amyloid Fibrils.

Amyloids are characterized by their capacity to bind Congo red (CR), one of the most used amyloid-specific dyes. The structural features of CR binding were unknown for years, mainly because of the lack of amyloid structures solved at high resolution. In the last few years, solid-state NMR spectroscopy enabled the determination of the structural features of amyloids, such as the HET-s prion forming domain (HET-s PFD), which also has recently been used to determine the amyloid-CR interface at atomic resolution. Herein, we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rationalize CR binding to amyloids. In contrast to a previous assumption on the binding mode, our results suggest that CR binding to the HET-s PFD involves a cooperative process entailing the formation of a complex with 1:1 stoichiometry. This provides a molecular basis to explain the bathochromic shift in the maximal absorbance wavelength when CR is bound to amyloids.

Pigmentation Chemistry and Radical-Based Collagen Degradation in Alkaptonuria and Osteoarthritic Cartilage.

Alkaptonuria (AKU) is a rare disease characterized by high levels of homogentisic acid (HGA); patients suffer from tissue ochronosis: dark brown pigmentation, especially of joint cartilage, leading to severe early osteoarthropathy. No molecular mechanism links elevated HGA to ochronosis; the pigment's chemical identity is still not known, nor how it induces joint cartilage degradation. Here we give key insight on HGA-derived pigment composition and collagen disruption in AKU cartilage. Synthetic pigment and pigmented human cartilage tissue both showed hydroquinone-resembling NMR signals. EPR spectroscopy showed that the synthetic pigment contains radicals. Moreover, we observed intrastrand disruption of collagen triple helix in pigmented AKU human cartilage, and in cartilage from patients with osteoarthritis. We propose that collagen degradation can occur via transient glycyl radicals, the formation of which is enhanced in AKU due to the redox environment generated by pigmentation.

Bioinspired and Mechanically Strong Fibers Based on Engineered Non-Spider Chimeric Proteins.

Silk-protein-based fibers have attracted considerable interest due to their low weight and extraordinary mechanical properties. Most studies on fibrous proteins focus on the recombinant spidroins, but these fibers exhibit moderate mechanical performance. Thus, the development of alternative structural proteins for the construction of robust fibers is an attractive goal. Herein, we report a class of biological fibers produced using a designed chimeric protein, which consists of the sequences of a cationic elastin-like polypeptide and a squid ring teeth protein. Remarkably, the chimeric protein fibers exhibit a breaking strength up to about 630 MPa and a corresponding toughness as high as about 130 MJ m-3 , making them superior to many recombinant spider silks and even comparable to some native counterparts. Therefore, this strategy is a novel concept for exploring bioinspired ultrastrong protein materials through the development of new types of structural chimeric proteins.

Theory of amyloid fibril nucleation from folded proteins.

We present a theoretical model for the nucleation of amyloid fibrils. In our model we use helix-coil theory to describe the equilibrium between a soluble native state and an aggregation-prone unfolded state. We then extend the theory to include oligomers with ß-sheet cores and calculate the free energy of these states using estimates for the energies of H-bonds, steric zipper interactions, and the conformational entropy cost of forming secondary structure. We find that states with fewer than ~10 ß-strands are unstable relative to the dissociated state and three ß-strands is the highest free energy state. We then use a modified version of Classical Nucleation Theory to compute the nucleation rate of fibrils from a supersaturated solution of monomers, dimers, and trimers. The nucleation rate has a non-monotonic dependence on denaturant concentration reflecting the competing effects of destabilizing the fibril and increasing the concentration of unfolded monomers. We estimate heterogeneous nucleation rates and discuss the application of our model to secondary nucleation.

Degree of Biomimicry of Artificial Spider Silk Spinning Assessed by NMR Spectroscopy.

Biomimetic spinning of artificial spider silk requires that the terminal domains of designed minispidroins undergo specific structural changes in concert with the ß-sheet conversion of the repetitive region. Herein, we combine solution and solid-state NMR methods to probe domain-specific structural changes in the NT2RepCT minispidroin, which allows us to assess the degree of biomimicry of artificial silk spinning. In addition, we show that the structural effects of post-spinning procedures can be examined. By studying the impact of NT2RepCT fiber drying, we observed a reversible beta-to-alpha conversion. We think that this approach will be useful for guiding the optimization of artificial spider silk fibers.

Binding Modes of Thioflavin†T on the Surface of Amyloid Fibrils Studied by NMR.

The mechanism for the interaction of thioflavin T (ThT) with amyloid fibrils at the molecular level is not known. Here, we used (1) H NMR spectroscopy to determine the binding mode of ThT on the surface of fibrils from lysozyme and insulin. Relayed rotating-frame Overhauser enhancements in ThT were observed, indicating that the orientation of ThT is orthogonal to the fibril surface. Importantly, the assembly state of ThT on both surfaces is different. On the surface of insulin fibrils, ThT is oligomeric, as indicated by rapid (1) H spin-lattice relaxation rate in the rotating frame (R1ρ ), presumably due to intermolecular dipole-dipole interactions between ThT molecules. In contrast, ThT on the surface of lysozyme fibrils is a monomer, as indicated by slower (1) H R1ρ . These results shed new light into the mechanism for the enhancement of ThT fluorescence and may lead to more efficient detectors of amyloid assemblies, which have escaped detection by ThT in monomer form.

Fibrous proteins: At the crossroads of genetic engineering and biotechnological applications.

Fibrous proteins, such as silk, elastin and collagen are finding broad impact in biomaterial systems for a range of biomedical and industrial applications. Some of the key advantages of biosynthetic fibrous proteins compared to synthetic polymers include the tailorability of sequence, protein size, degradation pattern, and mechanical properties. Recombinant DNA production and precise control over genetic sequence of these proteins allows expansion and fine tuning of material properties to meet the needs for specific applications. We review current approaches in the design, cloning, and expression of fibrous proteins, with a focus on strategies utilized to meet the challenges of repetitive fibrous protein production. We discuss recent advances in understanding the fundamental basis of structure-function relationships and the designs that foster fibrous protein self-assembly towards predictable architectures and properties for a range of applications. We highlight the potential of functionalization through genetic engineering to design fibrous protein systems for biotechnological and biomedical applications.

Effect of the surface chemistry of insulin fibrils on the aggregation rate.

Structure transition cascade: Insulin fibrils undergo a secondary structural transition-from the α-rich to the ß-rich form-upon progressively increasing the incubation time from 0.5 to ten hours. Atomic force microscopy measurements show that the fibril surface chemistry changes from hydrophilic to hydrophobic and the aggregation rate increases fivefold.

Nanofilament organization in highly tough fibers based on lamin proteins.

The escalating plastic pollution crisis necessitates sustainable alternatives, and one promising solution involves replacing petroleum-based polymers with fibrous proteins. This study focused on the recombinant production of intracellular fibrous proteins, specifically Caenorhabditis elegans lamin (Ce-lamin). Ce-lamins spontaneously organize within the cell nucleus, forming a network of nanofilaments. This intricate structure serves as an active layer that responds dynamically to mechanical strain and stress. Herein, we investigated the arrangement of nanofilaments into nanofibrils within wet-spun Ce-lamin fibers using alcoholic solutions as coagulants. Our goal was to understand their structural and mechanical properties, particularly in comparison with those produced with solutions containing Ca+2 ions, which typically result in the formation of nanofibrils with a collagen-like pattern. The introduction of ethanol solutions significantly altered this pattern, likely through rearrangement of the nanofilaments. Nevertheless, the resulting fibers exhibited superior toughness and strain, outperforming various synthetic fibers. The significance of the nanofilament structure in enhancing fiber toughness was emphasized through both the secondary structure transition during stretching and the influence of the Q159K point mutation. This study improves our understanding of the structural and mechanical aspects of Ce-lamin fibers, paving the way for the development of eco-friendly and high-quality fibers suitable for various applications, including medical implants and composite materials.

Mechanism and application of fibrous proteins in diabetic wound healing: a literature review.

Diabetic wounds are more complex than normal chronic wounds because of factors such as hypoxia, reduced local angiogenesis, and prolonged inflammation phase. Fibrous proteins, including collagen, fibrin, laminin, fibronectin, elastin etc., possess excellent inherent properties that make them highly advantageous in the area of wound healing. Accumulating evidence suggests that they contribute to the healing process of diabetic wounds by facilitating the repair and remodel of extracellular matrix, stimulating the development of vascular and granulation tissue, and so on. However, there is currently a lack of a comprehensive review of the application of these proteins in diabetes wounds. An overview of fibrous protein characteristics and the alterations linked to diabetic wounds is given in this article's initial section. Next is a summary of the advanced applications of fibrous proteins in the last five years, including acellular dermal matrix, hydrogel, foam, scaffold, and electrospun nanofibrous membrane. These dressings have the ability to actively promote healing in addition to just covering wounds compared to traditional wound dressings like gauze or bandage. Research on fibrous proteins and their role in diabetic wound healing may result in novel therapeutic modalities that lower the incidence of diabetic wounds and thereby enhance the health of diabetic patients.

Method of Using Raman Spectroscopy to Understand the Conformation of Fibrous Proteins.

Raman spectroscopy has been widely used in the research of fibrous proteins because of the insensitivity to moisture, less amount of sample, and better signal-to-noise ratio. In recent years, Raman spectroscopy is adopted to investigate the secondary structures of solid or aqueous protein, the conformation transition under different conditions (concentration, temperature, pressure, pH, chemical modification, external force, etc.), the orientation of the molecular chains, and some important chemical bonds. Here, we will introduce the methods for using Raman spectroscopy to analyze the conformation and orientation of samples, which would be an efficient method to get the "structure-property" relationship.

Gelation Methods to Assemble Fibrous Proteins.

Gelation is an efficient way to fabricate fibrous protein materials. Briefly, it is an aggregation process where protein molecules assembly from a random structure into an organized structure such as nanofibrillar networks. According to their mechanisms, the fibrous proteins gelation can be classified into physical gelation and chemical gelation. The physical gelation is formed by the conformational transformation of fibroin proteins, which can be triggered by temperature, concentration, pH, or shear force. On the other hand, the chemical gelation is to cross-link fibrous proteins through chemical and/or enzymatic reactions. In this chapter, we summarize the protocols for preparing fibrous protein hydrogels, including both physical and chemical methods. The mechanisms of these gelation methods are also highlighted.

Three-Dimensional Printing to Build Fibrous Protein Architectures.

Fibrous proteins are promising bioinks for three-dimensional printing techniques to fabricate sophisticated structures that find applications in both biomedical engineering and materials science. The critical point of manufacturing these fibrous protein inks is to adjust the cross-linking and rheology properties of proteins that matching the requirements of various printing techniques. In recent years, 3D printing techniques such as extrusion-based printing, droplet-based printing, and light-assisted printing techniques have widely been applied to build sophisticated fibrous protein architectures. In this regard, a series of fibrous protein-based bioinks have been developed, such as bioinks prepared from silk fibroin, collagen, fibrin, gelatin, and recombinant spider silk. In this chapter, we present the protocols to make various fibrous protein inks, as well as how to use these bioinks to print 3D structures via different printing techniques.

Synchrotron FTIR Microspectroscopy Methods to Understand the Conformation of Single Animal Silk Fibers.

Animal silks have received extensive attention in these years due to their unique mechanical properties. The study of the structure-property relationship of animal silks is not only critical for the understanding of the design secrets of natural materials but also can inspire the engineering material designs. Fourier transform infrared spectroscopy (FTIR) has been used to study the secondary structure of animal silk, which is considered to be critical to the mechanical properties of animal silk. However, most of these characterizations are conducted on silk fiber bundles. In this respect, synchrotron FTIR microspectroscopy (S-micro FTIR) has unique advantages in characterizing single animal silks, as S-micro FTIR has significant advantages in ultrahigh brightness and high spatial resolution to characterize samples with small size. Here, we will introduce the methods for using synchrotron FTIR microspectroscopy to analyze the conformation and orientation of single animal silk fibers, which would be an efficient method to elucidate the "structure-property" relationship within animal silks.

The byssus threads of Pinna nobilis: A histochemical and ultrastructural study.

The byssus of Pinna nobilis, the largest bivalve mollusc in the Mediterranean Sea, was investigated by histochemistry, immunohistochemistry, Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). At low magnification, the byssus threads appeared distinctively elliptical in cross-section, with a typical size approaching 50 x 25 micron and a featureless glassy appearance. Histochemical and immunohistochemical techniques confirmed the presence of elastic domains but the absence of collagen, which is known to be the main component in other molluscs. Ultrastructural analysis by TEM revealed the presence of at least two components within the thread, and an inner arrangement of straight, tightly packed longitudinal streaks. SEM observations while confirming the inner packing of straight, parallel subfibrils, suggested in the fracture surfaces the presence of unidentified substance which cemented together the same subfibrils and which was removed by exposure to extreme pH values. AFM micrographs added further evidence for the tight packing of subfibrils and provided some evidence of orthogonal, barely visible connecting structures. Finally, HCl or NaOH treatment left the subfibrils clean and free from any other component.Â.