Biosensor-based label-free assays of amyloid growth

Toward the equilibrium and kinetics of amyloid peptide self-assembly

Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.

Thermo-Responsive self-assembly of a dual glucagon-like peptide and glucagon receptor agonist

The human peptide hormone Oxyntomodulin (Oxm) is known to induce satiety, increase energy expenditure, and control blood glucose in humans, making it a promising candidate for treatment of obesity and/or type 2 diabetes mellitus. However, a pharmaceutical exploitation has thus far been impeded by fast in vivo clearance and the molecule's sensitivity to half-life extending structural modifications. We recently showed that Oxm self-assembles into amyloid-like nanofibrils that continuously release active, soluble Oxm in a peptide-deprived environment. S.c. injected Oxm nanofibrils extended plasma exposure from a few hours to five days in rodents, compared to s.c. applied soluble Oxm. Here we show that Oxm fibril elongation kinetics and thermodynamics display a uniquely low temperature optimum compared to previously reported amyloid-like peptide and protein assemblies. Elongation rate is optimal at room temperature, with association rates 2-3 times higher at 25 °C than at ≥37 °C or ≤20 °C. We deduce from a combination of Cryo electron microscopy and spectroscopic methods that Oxm fibrils have a double-layered, triangular cross-section composed of arch-shaped monomers. We suggest a thermodynamic model that links the necessary molecular rearrangements during fibrillation and peptide release to the unique temperature effects in Oxm self-assembly and disassembly.

Label-Free Protein Analysis Using Liquid Chromatography with Gravimetric Detection

The detection and analysis of proteins in a label-free manner under native solution conditions is an increasingly important objective in analytical bioscience platform development. Common approaches to detect native proteins in solution often require specific labels to enhance sensitivity. Dry mass sensing approaches, by contrast, using mechanical resonators, can operate in a label-free manner and offer attractive sensitivity. However, such approaches typically suffer from a lack of analyte selectivity as the interface between standard protein separation techniques and micro-resonator platforms is often constrained by qualitative mechanical sensor performance in the liquid phase. Here, we describe a strategy that overcomes this limitation by coupling liquid chromatography with a quartz crystal microbalance (QCM) platform by using a microfluidic spray dryer. We explore a strategy which allows first to separate a protein mixture in a physiological buffer solution using size exclusion chromatography, permitting specific protein fractions to be selected, desalted, and subsequently spray-dried onto the QCM for absolute mass analysis. By establishing a continuous flow interface between the chromatography column and the spray device via a flow splitter, simultaneous protein mass detection and sample fractionation is achieved, with sensitivity down to a 100 μg/mL limit of detection. This approach for quantitative label-free protein mixture analysis offers the potential for detection of protein species under physiological conditions.

Fabrication techniques of biomimetic scaffolds in three-dimensional cell culture: A review

In the last four decades, several researchers worldwide have routinely and meticulously exercised cell culture experiments in two-dimensional (2D) platforms. Using traditionally existing 2D models, the therapeutic efficacy of drugs has been inappropriately validated due to the failure in generating the precise therapeutic response. Fortunately, a 3D model addresses the foregoing limitations by recapitulating the in vivo environment. In this context, one has to contemplate the design of an appropriate scaffold for favoring the organization of cell microenvironment. Instituting pertinent model on the platter will pave way for a precise mimicking of in vivo conditions. It is because animal cells in scaffolds oblige spontaneous formation of 3D colonies that molecularly, phenotypically, and histologically resemble the native environment. The 3D culture provides insight into the biochemical aspects of cell-cell communication, plasticity, cell division, cytoskeletal reorganization, signaling mechanisms, differentiation, and cell death. Focusing on these criteria, this paper discusses in detail, the diversification of polymeric scaffolds based on their available resources. The paper also reviews the well-founded and latest techniques of scaffold fabrication, and their applications pertaining to tissue engineering, drug screening, and tumor model development.

Label-free, chronological and selective detection of aggregation and fibrillization of amyloid β protein in serum by microcantilever sensor immobilizing cholesterol-incorporated liposome

To facilitate the early diagnosis of Alzheimer's disease and mild cognitive impairment patients, we developed a cantilever-based microsensor that immobilized liposomes of various phospholipids to detect a trace amount of amyloid β (Aβ) protein, and investigated its aggregation and fibrillization on model cell membranes in human serum. Three species of liposomes composed of different phospholipids of 1,2-dipalmtoyl-sn-glycero-3-phosphocholine (DPPC), DPPC/phosphatidyl ethanolamine and 1,2-dipalmitoyl-sn-glycero-3-phosphorylglycerol having varied hydrophilic groups were applied, which showed different chronological interactions with Aβ(1-40) protein and varied sensitivities of the cantilever sensor, depending on their specific electrostatic charged conditions, hydrophilicity, and membrane fluidity. 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) having short hydrophobic carbon chains confirmed to show a large interaction with Aβ(1-40) and a high sensitivity. Furthermore, the incorporation of cholesterol into DMPC was effective to selectively detect Aβ(1-40) in human serum, which effect was also checked by quartz crystal microbalance. Finally, Aβ detection of 100-pM order was expected selectively in the serum by using the developed biosensor.

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Background

A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established.

Methods:

In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species.

Conclusion:

The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.

Versatile SPR aptasensor for detection of lysozyme dimer in oligomeric and aggregated mixtures

A Surface Plasmon Resonance (SPR) sensor for the quantitation of lysozyme dimer in monomer-dimer mixtures, reaching a detection limit of 1.4nM dimer, has been developed. The sensor is based on an aptamer which, although developed for the monomeric form, binds also the dimeric form but with a strikingly different kinetics. The aptasensor was calibrated using a dimer obtained by cross-linking. Sensorgrams acquired with the aptasensor in monomer-dimer mixtures were analysed using Principal Components Analysis and Multiple Regression to establish correlations with the dimer content in the mixtures. The method allows the detection of 0.1-1% dimer in monomer solutions without any separation. As an application, the aptasensor was used to qualitatively observe the initial stages of aggregation of lysozyme solutions at 60°C and pH 2, through the variations in lysozyme dimer amounts. Several other methods were used to characterize the lysozyme dimer obtained by cross-linking and confirm the SPR results. This work highlights the versatility of the aptasensor, which can be used, by simply tuning the experimental conditions, for the sensitive detection of either the monomer or the dimer and for the observation of the aggregation process of lysozyme.

Surface plasmon resonance for the label-free detection of Alzheimer's β-amyloid peptide aggregation

Amyloid peptide oligomers and fibrils are studied as targets for therapy and diagnosis of Alzheimer's disease. They are usually detected by amyloid incubation, but such method is necessarily associated with Aβ1-42 depletion and dye binding or conjugation, which have a complex influence on fibril growth, provide information about fibril elongation over long time periods only, and might lead to false-positive results in amyloid inhibition assay. Surface plasmon resonance (SPR) is used to study with no labelling and in real time the aggregation of Aβ1-42 amyloid on specific antibodies. SPR data show, for the first time by using SPR, a multi-phase association behavior for Aβ1-42 oligomers accounting for a sigmoidal growth of amyloid as a function of time, with two antibody-dependent aggregation patterns. The new method represents an advantageous alternative to traditional procedures for investigating amyloid self-assembly and inhibition from early-stage oligomer association, on the time scale of seconds to minutes, to long-term polymerization, on the time scale of hours to days.

Amyloid-β aggregation with gold nanoparticles on brain lipid bilayer

Understanding and manipulating amyloid-β (Aβ) aggregation provide key knowledge and means for the diagnosis and cure of Alzheimer's disease (AD) and the applications of Aβ-based aggregation systems. Here, we studied the formation of various Aβ aggregate structures with gold nanoparticles (AuNPs) and brain total lipid extract-based supported lipid bilayer (brain SLB). The roles of AuNPs and brain SLB in forming Aβ aggregates were studied in real time, and the structural details of Aβ aggregates were monitored and analyzed with the dark-field imaging of plasmonic AuNPs that allows for long-term in situ imaging of Aβ aggregates with great structural details without further labeling. It was shown that the fluid brain SLB platform provides the binding sites for Aβ and drives the fast and efficient formation of Aβ aggregate structures and, importantly, large Aβ plaque structures (>15 μm in diameter), a hallmark for AD, were formed without going through fibril structures when Aβ peptides were co-incubated with AuNPs on the brain SLB. The dark-field scattering and circular dichroism-correlation data suggest that AuNPs were heavily involved with Aβ aggregation on the brain SLB and less α-helix, less β-sheet and more random coil structures were found in large plaque-like Aβ aggregates.

The role of stable α-synuclein oligomers in the molecular events underlying amyloid formation

Studies of proteins' formation of amyloid fibrils have revealed that potentially cytotoxic oligomers frequently accumulate during fibril formation. An important question in the context of mechanistic studies of this process is whether or not oligomers are intermediates in the process of amyloid fibril formation, either as precursors of fibrils or as species involved in the fibril elongation process or instead if they are associated with an aggregation process that is distinct from that generating mature fibrils. Here we describe and characterize in detail two well-defined oligomeric species formed by the protein α-synuclein (αSN), whose aggregation is strongly implicated in the development of Parkinson's disease (PD). The two types of oligomers are both formed under conditions where amyloid fibril formation is observed but differ in molecular weight by an order of magnitude. Both possess a degree of β-sheet structure that is intermediate between that of the disordered monomer and the fully structured amyloid fibrils, and both have the capacity to permeabilize vesicles in vitro. The smaller oligomers, estimated to contain ∼30 monomers, are more numerous under the conditions used here than the larger ones, and small-angle X-ray scattering data suggest that they are ellipsoidal with a high degree of flexibility at the interface with solvent. This oligomer population is unable to elongate fibrils and indeed results in an inhibition of the kinetics of amyloid formation in a concentration-dependent manner.

Resolution enhancement of suspended microchannel resonators for weighing of biomolecular complexes in solution

We introduce the use of correlation analysis to extend the dynamic range of suspended micro- and nanochannel resonator (SMR/SNR) mass sensors by over five orders of magnitude. This method can analyze populations of particles flowing through an embedded channel micromechanical resonator, even when the individual particle masses are far below the noise floor. To characterize the method, we measured the mass of polystyrene nanoparticles with 300 zg resolution. As an application, we monitored the time course of insulin amyloid formation from pre-fibrillar aggregates to mature fibrils of 15 MDa average mass. Results were compared with thioflavin-T (ThT) assays and electron microscopy (EM). Mass measurements offer additional information over ThT during the fluorescent inaccessible lag period, and the average fibril dimensions calculated from the mass signal are in good accordance with EM. In the future, we envision that more detailed modeling will allow the computational deconvolution of multicomponent samples, enabling the mass spectrometric characterization of a variety of biomolecular complexes, small organelles, and nanoparticles in solution.

Novel insights into amylin aggregation

Amylin is a peptide that aggregates into species that are toxic to pancreatic beta cells, leading to type II diabetes. This study has for the first time quantified amylin association and dissociation kinetics (association constant (ka ) = 28.7 ± 5.1 L mol-1 s-1 and dissociation constant (kd ) = 2.8 ± 0.6 ×10-4 s-1) using surface plasmon resonance (SPR). Thus far, techniques used for the sizing of amylin aggregates do not cater for the real-time monitoring of unconstrained amylin in solution. In this regard we evaluated recently innovated nanoparticle tracking analysis (NTA). In addition, both SPR and NTA were used to study the effect of previously synthesized amylin derivatives on amylin aggregation and to evaluate their potential as a cell-free system for screening potential inhibitors of amylin-mediated cytotoxicity. Results obtained from NTA highlighted a predominance of 100-300 nm amylin aggregates and correlation to previously published cytotoxicity results suggests the toxic species of amylin to be 200-300 nm in size. The results seem to indicate that NTA has potential as a new technique to monitor the aggregation potential of amyloid peptides in solution and also to screen potential inhibitors of amylin-mediated cytotoxicity.

A label-free electrical assay of fibrous amyloid β based on semiconductor biosensing

Simple electrical assay discriminates between fibrous and non-fibrous amyloid β (Aβ) proteins, and determines the fibrous Aβ concentration with high sensitivity.

Fibrillogenesis of human β2 -microglobulin in three-dimensional silicon microstructures

The authors describe the interaction of biological nanostructures formed by β(2) -microglobulin amyloid fibrils with three-dimensional silicon microstructures consisting in periodic arrays of vertical silicon walls (≈3 μm-thick) separated by 50 μm-deep air gaps (≈5 μm-wide). These structures are of great interest from a biological point of view since they well mimic the interstitial environment typical of amyloid deposition in vivo. Moreover, they behave as hybrid photonic crystals, potentially applicable as optical transducers for label-free detection of the kinetics of amyloid fibrils formation. Fluorescence and atomic force microscopy (AFM) show that a uniform distribution of amyloid fibrils is achieved when fibrillogenesis occurs directly on silicon. The high resolution AFM images also demonstrate that amyloid fibrils grown on silicon are characterized by the same fine structure typically ensured by fibrillogenesis in solution.

Protein solubility and protein homeostasis: a generic view of protein misfolding disorders

According to the "generic view" of protein aggregation, the ability to self-assemble into stable and highly organized structures such as amyloid fibrils is not an unusual feature exhibited by a small group of peptides and proteins with special sequence or structural properties, but rather a property shared by most proteins. At the same time, through a wide variety of techniques, many of which were originally devised for applications in other disciplines, it has also been established that the maintenance of proteins in a soluble state is a fundamental aspect of protein homeostasis. Taken together, these advances offer a unified framework for understanding the molecular basis of protein aggregation and for the rational development of therapeutic strategies based on the biological and chemical regulation of protein solubility.

Probing small molecule binding to amyloid fibrils

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.

Surface plasmon resonance based biosensors for exploring the influence of alkaloids on aggregation of amyloid-β peptide

The main objective of the presented study was the development of a simple analytical tool for exploring the influence of naturally occurring compounds on the aggregation of amyloid-β peptide (Aβ₄₀) in order to find potential anti-neurodegenerative drugs. The gold discs used for surface plasmon resonance (SPR) measurements were modified with thioaliphatic acid. The surface functionalized with carboxylic groups was used for covalent attaching of Aβ₄₀ probe by creation of amide bonds in the presence of EDC/NHS. The modified SPR gold discs were used for exploring the Aβ₄₀ aggregation process in the presence of selected alkaloids: arecoline hydrobromide, pseudopelletierine hydrochloride, trigonelline hydrochloride and α-lobeline hydrochloride. The obtained results were discussed with other parameters which govern the phenomenon studied such as lipophilicity/hydrophilicy and Aβ₄₀-alkaloid association constants.

Relationship between prion propensity and the rates of individual molecular steps of fibril assembly

Peptides and proteins possess an inherent propensity to self-assemble into generic fibrillar nanostructures known as amyloid fibrils, some of which are involved in medical conditions such as Alzheimer disease. In certain cases, such structures can self-propagate in living systems as prions and transmit characteristic traits to the host organism. The mechanisms that allow certain amyloid species but not others to function as prions are not fully understood. Much progress in understanding the prion phenomenon has been achieved through the study of prions in yeast as this system has proved to be experimentally highly tractable; but quantitative understanding of the biophysics and kinetics of the assembly process has remained challenging. Here, we explore the assembly of two closely related homologues of the Ure2p protein from Saccharomyces cerevisiae and Saccharomyces paradoxus, and by using a combination of kinetic theory with solution and biosensor assays, we are able to compare the rates of the individual microscopic steps of prion fibril assembly. We find that for these proteins the fragmentation rate is encoded in the structure of the seed fibrils, whereas the elongation rate is principally determined by the nature of the soluble precursor protein. Our results further reveal that fibrils that elongate faster but fracture less frequently can lose their ability to propagate as prions. These findings illuminate the connections between the in vitro aggregation of proteins and the in vivo proliferation of prions, and provide a framework for the quantitative understanding of the parameters governing the behavior of amyloid fibrils in normal and aberrant biological pathways.

Studying the effects of chaperones on amyloid fibril formation

The results of cell and animal model studies demonstrate that molecular chaperones play an important role in controlling the processes of protein misfolding and amyloid formation in vivo. In addition, chaperones are involved in the appearance, propagation and clearance of prion phenotypes in yeast. The effect of chaperones on amyloid formation has been studied in great detail in recent years in order to elucidate the underlying mechanisms. An important approach is the direct study of effects of chaperones on amyloid fibril formation in vitro. This review introduces the methods and techniques that are commonly used to control and monitor the time course of fibril formation, and to detect interactions between chaperones and fibril-forming proteins. The techniques we address include thioflavin T binding fluorescence and filter retardation assays, size-exclusion chromatography, dynamic light scattering, and biosensor assays. Our aim in this review is to provide guidance on how to embark on study of the effect of chaperones on amyloid fibril formation, and how to avoid common problems that may be encountered, using examples and experience from the authors' lab and from the wider literature.