Structural evaluation of an amyloid fibril model using small-angle x-ray scattering

Complexes of soybean protein fibrils and chlorogenic acid: Interaction mechanism and antibacterial activity

This study explored the mechanism of interaction between chlorogenic acid (CA) and protein fibrils (PF) as well as the effects of varying the CA/PF concentration ratio on antibacterial activity. Analysis of various parameters, such as ζ-potential, thioflavin T fluorescence intensity, surface hydrophobicity, and free sulfhydryl groups, revealed that the interaction between PF and CA altered the structure of PF. Fluorescence analysis revealed that hydrogen bonding and hydrophobic interactions were the primary interaction forces causing conformational rearrangement, resulting in a shorter, more flexible, and thicker fibril structure, as observed through transmission electron microscopy. Fourier-transform infrared spectroscopy, small-angle X-ray scattering, and X-ray diffraction analyses revealed that the characteristic fibril structure was destroyed when the CA/PF ratio exceeded 0.05. Notably, the CA-PF complexes inhibited the growth of Escherichia coli and Staphylococcus aureus and also exhibited antioxidant activity. Overall, this study expands the application prospects of CA and PF in the food industry.

Catalytic physiological amyloids

Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.

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

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

Mechano-Chemistry across Phase Transitions in Heated Albumin Protein Solutions

The presence of certain proteins in biofluids such as synovial fluid, blood plasma, and saliva gives these fluids non-Newtonian viscoelastic properties. The amount of these protein macromolecules in biofluids is an important biomarker for the diagnosis of various health conditions, including Alzheimer's disease, cardiovascular disorders, and joint quality. However, existing technologies for measuring the behavior of macromolecules in biofluids have limitations, such as long turnaround times, complex protocols, and insufficient sensitivity. To address these issues, we propose non-contact, optical Brillouin and Raman spectroscopy to assess the viscoelasticity and chemistry of non-Newtonian solutions, respectively, at different temperatures in several minutes. In this work, bovine and human serum albumin solution-based biopolymers were studied to obtain both their collective dynamics and molecular chemical evolution across heat-driven phase transitions at various protein concentrations. The observed phase transitions at elevated temperatures could be fully delayed in heated biopolymers by appropriately raising the level of protein concentration. The non-contact optical monitoring of viscoelastic and chemical property evolution could represent novel potential mechano-chemical biomarkers for disease diagnosis and subsequent treatment applications, including hyperthermia.

Thermoresponsive BSA hydrogels with phase tunability

Amyloids are fibrillar structures formed due to protein aggregation or misfolding when the molecules undergo a conformational change from α-helix to β-sheet. Although this self-assembly is associated with many neurodegenerative diseases in vivo, the highly ordered amyloidic structures formed in vitro are ideal scaffolds for many bionanotechnological applications. Amyloid fibrillar networks under specific stimuli can also form stable hydrogels. We have used bovine serum albumin (BSA) as a model amyloidogenic protein to obtain thermally-induced hydrogels that display tunable sol-gel-sol transitions spanning over minutes to days. High concentrations of BSA (14-22% w/v) were heated at 65 °C for less than 3 min without any cross-linking agent to yield soft, injectable gels that were non-toxic to mammalian cells. A detailed investigation of temperature, concentration, incubation time and ionic strength on the formation and reversal of these gels was carried out using visual inspection, rheology, electron microscopy, fluorescence spectroscopy, UV-visible spectroscopy and circular dichroism spectroscopy. The optimum gelation temperature (T_g) for phase reversal of BSA gels was found to lie between 60 and 70 °C. An increase in protein concentration led to a reduction in the gelation time and increase in the gel-to-rev sol transition time. Gels heated for longer duration than their minimum gelation time yielded irreversible gels suggesting that low incubation periods were favourable for partial protein denaturation and hydrogel formation. This was supported by time-resolved secondary and tertiary structural ensemble studies. Further, the hydrogel networks demonstrated a zero-order drug release kinetics and the rev sol was found to be cytocompatible with HaCaT skin cell lines. Overall, our approach demonstrates rapid, crosslinker-free thermoresponsive BSA gelation with wide tunability and control on the time and material property, ideal for topical drug delivery applications.

Feasibility of imaging amyloid in the brain using small-angle x-ray scattering

Small-angle x-ray scattering (SAXS) imaging may have the potential to imageβ-amyloid plaquesin vivoin the brain without tracers for assessment of Alzheimer's disease (AD). We use a laboratory SAXS system for planar imaging of AD model and control mouse brains slices to detect regions with high density of amyloid plaques. These regions were validated with histology methods. Using Monte Carlo techniques, we simulate SAXS computed tomography (SAXS-CT) system to study the potential of selectively differentiating amyloid targets in mouse and human head phantoms with detailed anatomy. We found contrast between amyloid and brain tissue at smallq(below 0.8 nm^-1) in the neocortex region of the transgenic brain slices as supported by histology. We observed similar behavior through planar SAXS imaging of an amyloid-like fibril deposit with a 0.8 mm diameter at a known location on a wild type mouse brain. In our SAXS-CT simulations, we found that 33-keV x rays provide increase plaque visibility in the mouse head for targets of at least 0.1 mm in diameter, while in the human head, 70-keV x rays were capable of detecting plaques as small as 2 mm. To increase radiation efficiency, we used a weighted-sum image visualization approach allowing the dose deposited by 70-keV x rays per SAXS-CT slice of the human head to be reduced by a factor of 10 to 71 mGy for gray matter and 63 mGy for white matter. The findings suggest that a dedicated SAXS-CT system forin vivoamyloid imaging in small animals and humans can be successfully developed with further system optimization to detect regions with amyloid plaques in the brain with a safe level of radiation dose.

Feasibility of a label-free X-ray method to estimate brain amyloid load in small animals

BACKGROUND

Amyloid plaque in the brain is associated with a wide range of neurodegenerative diseases such as Alzheimer's and Parkinson's and defined as aggregates of amyloid fibrils rich in β-sheet structures.

NEW METHOD

We report a label-free method based on small-angle X-ray scattering (SAXS) to estimate amyloid load in an intact mouse head with skull. The method is based on recording and analyzing the X rays elastically scattered from the β-sheets of amyloid plaques in a mouse head at angles smaller than 10° and energies between 30 and 45 keV. The method is demonstrated by acquiring the spectral SAXS data of an amyloid model and an excised head from a wild-type mouse for 600 s.

RESULTS

We captured the distinct scattering peaks of the amyloid plaques at momentum transfer (q) of 6 and 13 nm^-1 associated with β-sheet structure. We first show linear correlation between the mass fraction of the amyloid target and the area under the peak (AUP) of the scattering curve. We report results for estimating amyloid load in a fixed mouse head by recovering the characteristic scattering signal from the amyloid target situated at various locations. The coefficient of variation in the amyloid load estimate is found to be less than 10%.

COMPARISON WITH EXISTING METHODS

There are no previously described label-free X-ray methods for the estimation of amyloid load in an intact head.

CONCLUSIONS

We demonstrated the feasibility of a label-free method based on SAXS to potentially estimate brain amyloid in small animals.

Small-angle X-ray scattering characterization of a [Formula: see text]-amyloid model in phantoms

OBJECTIVE

We present a method to prepare an amyloid model at scalable quantities for phantom studies to evaluate small-angle x-ray scattering systems for amyloid detection. Two amyloid models were made from a plasma protein with and without heating. Both models mimic the [Formula: see text]-sheet structure of the [Formula: see text]-amyloid ([Formula: see text]) plaques in Alzheimer's disease. Amyloid detection is based on the distinct peaks in the scattering signature of the [Formula: see text]-sheet structure. We characterized the amyloid models using a spectral small-angle x-ray scattering (sSAXS) prototype with samples in a plastic syringe and within a cylindrical polymethyl methacrylate (PMMA) phantom.

RESULTS

sSAXS data show that we can detect the scattering peaks characteristic of amyloid [Formula: see text]-sheet structure in both models around 6 and 13 [Formula: see text]. The [Formula: see text] model prepared without heating provides a stronger signal in the PMMA phantom. The methods described can be used to prepare models in sufficiently large quantities and used in samples with different packing density to assess the performance of [Formula: see text] quantification systems.

Battacin-Inspired Ultrashort Peptides: Nanostructure Analysis and Antimicrobial Activity

Peptides can serve as versatile therapeutics with a highly modular structure and tunable biophysical properties. In particular, the efficacy of peptide antibiotics against drug-resistant pathogens is of great promise, as few new classes of antibiotics are being developed to overcome the ever-increasing bacterial resistance to contemporary drugs. This work reports biophysical and antimicrobial studies of a designed library of ultrashort peptides that self-assemble into hydrogels at concentrations as low as 0.5% w/v in buffered saline, as confirmed by rheology. The hydrogels are constituted by β-sheet-rich nanofibril networks, as determined by biophysical techniques including spectroscopy (attenuated total reflectance Fourier transform infrared spectroscopy and Congo red binding assay), short- and wide-angle X-ray scattering, and electron microscopy. Both peptide solutions and self-assembled hydrogels show potent antimicrobial activity against S. aureus and Pseudomonas aeruginosa by membrane lysis. These peptides also displayed selectivity toward bacterial cells over human dermal fibroblasts in vitro, as determined from Live/Dead, scanning electron microscopy, and coculture assays. This work reports an antimicrobial self-assembling motif of only three residues comprising an aromatically acylated cationic d-Dab/Lys amino acid, a second cationic residue, and naphthylalanine that heavily influences the self-assembly of these peptides into hydrogels. The variations in the antimicrobial activity and self-assembly properties between analogues may have implications in future studies on the correlation between self-assembly and biological activity in ultrashort peptides.

Atomic force microscopy for single molecule characterisation of protein aggregation

The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials.

Congo Red and amyloids: history and relationship

Staining with Congo Red (CR) is a qualitative method used for the identification of amyloids in vitro and in tissue sections. However, the drawbacks and artefacts obtained when using this dye can be found both in vitro and in vivo. Analysis of scientific data from previous studies shows that CR staining alone is not sufficient for confirmation of the amyloid nature of protein aggregates in vitro or for diagnosis of amyloidosis in tissue sections. In the present paper, we describe the characteristics and limitations of other methods used for amyloid studies. Our historical review on the use of CR staining for amyloid studies may provide insight into the pitfalls and caveats related to this technique for researchers considering using this dye.

Comparative experiments of fibril formation from whey protein concentrate with homogeneous and secondary nuclei

Two types of special structures, homogeneous and secondary nuclei, form during fibril formation. The structural and functional properties of amyloid fibrils in whey protein concentrate (WPC) with different ratios of added homogeneous nuclei to secondary nuclei were investigated. Thioflavin T fluorescence analysis and kinetic equations indicated that two types of nuclei could accelerate WPC fibrillation compared with WPC self-assembling into amyloid fibrils, thereby reducing the lag time and increasing the number of fibrils. However, there were considerable differences in the nucleation-inducing capability of WPC fibrillation between homogeneous and secondary nuclei. The number of fibrils formed by adding homogeneous nuclei was higher than that obtained with secondary nuclei, the increase in the Th T fluorescence intensity induced by homogeneous nuclei was 1.83-fold much than secondary nuclei. Meanwhile, secondary nuclei yielded a 2.71-fold faster aggregation rate of WPC than homogeneous nuclei, particularly during the first hour of thermal treatment (protein mass ratio of nuclei to WPC 1:1). The gelation time of WPC after secondary nuclei addition was shorter, from 10 h (WPC (2.0/6.5)) to 4 h (WPC + HN) to 2 h (WPC + SN); however, the gel microstructure of WPC after the addition of homogeneous nuclei was denser, yielding a preferred water holding capacity.

Small-angle X-ray scattering characteristics of mouse brain: Planar imaging measurements and tomographic imaging simulations

Small-angle x-ray scattering (SAXS) imaging can differentiate tissue types based on their nanoscale molecular structure. However, characterization of the coherent scattering cross-section profile of relevant tissues is needed to optimally design SAXS imaging techniques for a variety of biomedical applications. Reported measured nervous tissue x-ray scattering cross sections under a synchrotron source have had limited agreement. We report a set of x-ray cross-section measurements obtained from planar SAXS imaging of 1 mm thick mouse brain (APP/PS1 wild-type) coronal slices using an 8 keV laboratory x-ray source. Two characteristic peaks were found at 0.96 and 1.60 nm⁻¹ attributed to myelin. The peak intensities varied by location in the slice. We found that regions of gray matter, white matter, and corpus callosum could be segmented by their increasing intensities of myelin peaks respectively. Measured small-angle x-ray scattering cross sections were then used to define brain tissue scattering properties in a GPU-accelerated Monte Carlo simulation of SAXS computed tomography (CT) using a higher monochromatic x-ray energy (20 keV) to study design trade-offs for noninvasive in vivo SAXS imaging on a small-animal head including radiation dose, signal-to-noise ratio (SNR), and the effect of skull presence on the previous two metrics. Simulation results show the estimated total dose to the mouse head for a single SAXS-CT slice was 149.4 mGy. The pixel SNR was approximately 30.8 for white matter material whether or not a skull was present. In this early-stage proof-of-principle work, we have demonstrated our brain cross-section data and simulation tools can be used to assess optimal instrument parameters for dedicated small-animal SAXS-CT prototypes.