1. Aggregation assays on fluorescence plate readers
NOTE: The protocol described here is an example of how to study the aggregation of any protein or peptide by chemical kinetics. In particular, it describes an optimized protocol to study the aggregation of the Aβ42 peptide, which is involved in the onset and progression of Alzheimer’s disease58,59. A similar protocol can be adjusted and adopted towards studying the aggregation of any protein or peptide.
2. Sample preparation for AFM and nano-IR measurements
3. AFM imaging of the morphology of protein aggregates
NOTE: Morphology measurements can be performed both in contact and dynamic mode, in the following steps the latter is described since it reduces lateral forces to measure the 3D morphology of the sample with high resolution. AFM-IR measurements will be performed in contact mode to enhance AFM-IR signal-to-noise ratio.
4. Infrared nanospectroscopy measurements of protein aggregates
5. Image processing and analysis of cross-sectional dimensions
A representative time course of Aβ42 aggregation, as measured by the ThT fluorescence assay, is shown in Figure 1. The aggregation process is commonly characterized by a sigmoidal curve, where a lag phase is initially observed, and is followed by a steep growth phase, before the curve reaches a plateau when an equilibrium steady state is reached6,7,58. It is essential to ensure that an optimized aggregation protocol is used to generate high-quality data to study the molecular details pertaining to aggregation processes58.
High resolution of AFM enables to investigate the morphology and heterogeneity of the aggregated species at different time points of the process. During the aggregation, monitored by the ThT assay, aliquots of the sample in the plates are prepared for single aggregate investigation by AFM and nano-IR (Figure 1). The typical process flow of manual sample preparation is shown in Figure 2. At the completion of the measurement of the 3D morphology of the sample by high resolution and phase-controlled AFM, the maps are flattened to remove non-linearity of the piezoelectric scanner and reduce sources of error in post-processing analysis of sample morphology (Figure 3). Subsequently, an accurate and sensitive single molecule statistical analysis can be performed, as shown in Figure 4. From a 3D morphology map, it is possible to extract aggregate cross-sectional height, width and length (or diameter in case of spheroidal particles), which allows to distinguish and characterize distinct species of aggregates present during the aggregation time course23,38. Typical time points of interest to investigate the process of aggregation are the lag phase, the growth phase and the plateau phase (Figure 1). During the lag phase, monomeric and oligomeric species of Aβ42 are primarily present. When visualized by AFM, monomeric and oligomeric species of Aβ42 typically appear as spheroidal particles 1−15 nm in diameter and 0.3−2 nm in height (Figure 1, bottom left)38,39. Formation of elongated protofilaments, protofibrils and fibrils is visible during the growth phase of Aβ42 aggregation time course (Figure 1, bottom middle)38,39. Typically, protofilaments appear as elongated features hundreds of nanometers in length and 0.5−2 nm in height, while protofibrils appear as elongated linear or curvilinear aggregates 1−5 nm in height and hundreds of nanometers in length38,39. During the plateau phase, fibrils are the dominant species of Aβ42 aggregates. Aβ42 fibrils typically appear as unbranched, thread-like structures, with a cross-sectional diameter of 6−10 nm and length in the order if micrometers (Figure 3, bottom right)38,39. Remarkably, this schematic representation of the morphological properties of the aggregates is a general feature of most aggregating proteins and peptides13,14.
After the investigation of the sample morphology, nano-IR can be used to investigate the chemical properties of the individual protein aggregate species present during the process of aggregation, by acquiring nanoscale-resolved IR maps and spectra both in air and native liquid environment24,26,38,4249,50,51,52,. Figure 5 shows a schematic illustration of the AFM-IR setup. An IR source is used to illuminate the sample from the bottom in total internal reflection or directly from the top as in Figure 5a. If the IR light is absorbed by the sample, it will excite the corresponding molecular vibrational energy transition levels of the species present. The vibrational energy is dissipated inside the sample in the form of thermal heating, which causes the thermal expansion of the sample. This expansion is measured at the nanoscale by the AFM tip in contact with the sample with a resolution in the order of 10 nm. At each pulse, the cantilever detects the thermal expansion. In particular, the fast expansion of the sample kicks out the cantilever from contact with the sample, and after the kick out the cantilever rings down at its natural frequencies. In order to enhance the sensitivity of AFM-IR, it is possible to tune the laser pulse frequency at the same frequency of the oscillation of the cantilever54. In order to work in this resonance-enhanced mode, it is necessary to have IR sources that can be pulsed in a wide range of frequencies, such as quantum cascade lasers that operate typically in a range between 1−1000 kHz. The peak-to-peak amplitude and the fast Fourier transform of the ringdown signal, termed IR amplitude, of the raw cantilever deflection are proportional to the IR light absorbed. These signals are detected in real time by measuring the deflection of a red laser focused on the top of the cantilever. In order to acquire chemical maps, the laser wavenumber is fixed at a certain wavenumber and the IR amplitude signal is collected at each point of the map, while, to acquire IR spectra, the position of the cantilever is fixed in a position of interest and the laser wavelength is swept along the spectroscopic range of interest. The ultimate resolution of AFM-IR enables the measurement of the chemical properties of protein aggregates with a cross-sectional height of approximately 5 nm, as represented in Figure 6.
Figure 1: Monitoring of the aggregation time course in vitro via ThT fluorescence and AFM.
Samples taken during the lag phase, growth phase, and plateau phase of the aggregation process as detected by ThT fluorescence were imaged via high-resolution AFM. This figure has been adapted from Ruggeri et al.38. Please click here to view a larger version of this figure.
Figure 2: Schematic representation of the substrate preparation and sample deposition for AFM measurements.
(A, B) Mica etching using adhesive tape. (C) Sample deposition. (D) Sample incubation. (E) Sample rinsing with ultrapure water. (F) Sample drying under gentle flow of nitrogen. (G) Sample imaging using microfabricated AFM cantilever with sharp tip on its end. (H) Processed image of amyloid fibrils. Please click here to view a larger version of this figure.
Figure 3: AFM image processing procedure42.
The top of each panel shows a profile line of the sample surface (red line) illustrated by the corresponding AFM image, while the lower part shows a histogram of the height of all pixels in the image. (a) Raw AFM image before image flattening procedure. (b) AFM image after the processing procedure using the whole plane flattening. Fibrillar structures (pink color) were masked from the flattening procedure. (c) Image processed using line-by-line flattening procedure. (d) Final image after the image processing procedure. This figure has been adapted from Ruggeri et al.42.
Figure 4: Single aggregate statistical analysis of AFM images.
(a) Example of the tracing of the heights and lengths of fibrillar structures, indicated with 1 and 2. (b) Graph with sections of the traced fibrils and their average height. (c) Example of a histogram showing the average height of fibrillar structures. (d) Graph with normalized profile of the traced fibrils 1 and 2. (e) Histogram distribution of the normalized profile height points. This figure has been adapted from Ruggeri et al.42. Please click here to view a larger version of this figure.
Figure 5: Principle of function of the AFM-IR method.
(a) Absorbed IR light causes the thermal expansion of the sample, exciting the mechanical resonances of the AFM cantilever in contact with the sample. The amplitude of the cantilever oscillations is proportional to the IR absorption. (b) IR absorption maps are obtained scanning the cantilever on the sample while fixing the laser wavelength. (c) Tip and sample in contact behave as a system of coupled springs whose resonant frequency increases monotonically with the intrinsic stiffness of the sample50. (d) Localized spectra are obtained by sweeping the laser wavelength while fixing the position of the AFM cantilever. (e) IR spectrum of protein. (f) In summary, AFM-IR enables the simultaneous study of morphological, mechanical and chemical properties at the nanoscale26. Please click here to view a larger version of this figure.
Figure 6: Infrared nanospectroscopy (nano-IR) of a single amyloid aggregate.
(a) AFM morphology map. (b) IR absorption map at the laser resonance peak at 1658 cm-1. (c) Cross sectional dimensions of the fibril height. (d) IR spectra on different positions of the fibrillar structure (marked in panel b with blue circles) and the substrate (marked in panel b with green circles). The average net signal deriving from the aggregate structure (solid black line) was obtained by subtracting the averaged background signal (solid green line) from the averaged fibril signal (solid blue line). This figure has been adapted from Ruggeri et al.42.
AFM-IR system | Anasys Instruments | nanoIR 2 or 3 | Systems to measure thermal expansion in contact and resonance mode |
Corning 96-well Half Area Black/Clear Bottom Polystyrene NBS Microplate | Corning | 3881 | |
Corning Microplate Aluminium Sealing Tape | Corning | 6570 | |
Double Sided Adhesive Discs | AGAR Scientific | AGG3347N | |
FLUOstar Omega | BMG Labtech | 415-101 | Platereader |
Mica Disc 10mm V1 | AGAR Scientific | AGF7013 | |
Park NX10 AFM system | Park Systems | N/A | Atomic Force Microscope |
Platypus Ultra-Flat Gold Chips | Platypus Technologies | AU.1000.SWTSG | |
PPP-NCHR-10 cantilevers | Park Systems | PPP-NCHR-10 | |
Protein LowBind Tubes, 2.0mL | Eppendorf | 30108132 | |
Silicon gold coated cantilevers | Anasys Instruments | PR-EX-nIR2 | |
SPM Specimen Discs 12mm | AGAR Scientific | AGF7001 |
The phenomenon of protein misfolding and aggregation results in the formation of highly heterogeneous protein aggregates, which are associated with neurodegenerative conditions such as Alzheimer’s and Parkinson’s diseases. In particular low molecular weight aggregates, amyloid oligomers, have been shown to possess generic cytotoxic properties and are implicated as neurotoxins in many forms of dementia. We illustrate the use of methods based on atomic force microscopy (AFM) to address the challenging task of characterizing the morphological, structural and chemical properties of these aggregates, which are difficult to study using conventional structural methods or bulk biophysical methods because of their heterogeneity and transient nature. Scanning probe microscopy approaches are now capable of investigating the morphology of amyloid aggregates with sub-nanometer resolution. We show here that infrared (IR) nanospectroscopy (AFM-IR), which simultaneously exploits the high resolution of AFM and the chemical recognition power of IR spectroscopy, can go further and enable the characterization of the structural properties of individual protein aggregates, and thus offer insights into the aggregation mechanisms. Since the approach that we describe can be applied also to the investigations of the interactions of protein assemblies with small molecules and antibodies, it can deliver fundamental information to develop new therapeutic compounds to diagnose or treat neurodegenerative disorders.
The phenomenon of protein misfolding and aggregation results in the formation of highly heterogeneous protein aggregates, which are associated with neurodegenerative conditions such as Alzheimer’s and Parkinson’s diseases. In particular low molecular weight aggregates, amyloid oligomers, have been shown to possess generic cytotoxic properties and are implicated as neurotoxins in many forms of dementia. We illustrate the use of methods based on atomic force microscopy (AFM) to address the challenging task of characterizing the morphological, structural and chemical properties of these aggregates, which are difficult to study using conventional structural methods or bulk biophysical methods because of their heterogeneity and transient nature. Scanning probe microscopy approaches are now capable of investigating the morphology of amyloid aggregates with sub-nanometer resolution. We show here that infrared (IR) nanospectroscopy (AFM-IR), which simultaneously exploits the high resolution of AFM and the chemical recognition power of IR spectroscopy, can go further and enable the characterization of the structural properties of individual protein aggregates, and thus offer insights into the aggregation mechanisms. Since the approach that we describe can be applied also to the investigations of the interactions of protein assemblies with small molecules and antibodies, it can deliver fundamental information to develop new therapeutic compounds to diagnose or treat neurodegenerative disorders.
The phenomenon of protein misfolding and aggregation results in the formation of highly heterogeneous protein aggregates, which are associated with neurodegenerative conditions such as Alzheimer’s and Parkinson’s diseases. In particular low molecular weight aggregates, amyloid oligomers, have been shown to possess generic cytotoxic properties and are implicated as neurotoxins in many forms of dementia. We illustrate the use of methods based on atomic force microscopy (AFM) to address the challenging task of characterizing the morphological, structural and chemical properties of these aggregates, which are difficult to study using conventional structural methods or bulk biophysical methods because of their heterogeneity and transient nature. Scanning probe microscopy approaches are now capable of investigating the morphology of amyloid aggregates with sub-nanometer resolution. We show here that infrared (IR) nanospectroscopy (AFM-IR), which simultaneously exploits the high resolution of AFM and the chemical recognition power of IR spectroscopy, can go further and enable the characterization of the structural properties of individual protein aggregates, and thus offer insights into the aggregation mechanisms. Since the approach that we describe can be applied also to the investigations of the interactions of protein assemblies with small molecules and antibodies, it can deliver fundamental information to develop new therapeutic compounds to diagnose or treat neurodegenerative disorders.