Characterizing Individual Protein Aggregates by Infrared Nanospectroscopy and Atomic Force Microscopy

Summary

We describe the application of infrared nanospectroscopy and high-resolution atomic force microscopy to visualize the process of protein self-assembly into oligomeric aggregates and amyloid fibrils, which is closely associated with the onset and development of a wide range of human neurodegenerative disorders.

Abstract

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.

Introduction

Over 40 million people worldwide are currently affected by neurodegenerative disorders, such as Alzheimer’s (AD)¹ and Parkinson’s (PD)² diseases. More generally, more than fifty pathologies are associated at the molecular level with protein misfolding and aggregation, a process that leads to the proliferation of insoluble fibrillar protein aggregates, known as amyloid deposits^3,4. The molecular origins of neurodegeneration and its links with protein conformational changes of proteins leading to amyloid formation, however, remain unclear, in large part....

Protocol

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 disease^58,59. A similar protocol can be adjusted and adopted towards studying the aggregatio.......

Discussion

The first critical step in this protocol is the preparation of monomeric proteins, such as in the case of Aβ42 solution described in steps 1.1 and 1.2. It is essential to initiate the aggregation process from a highly pure, monomeric solution, as the presence of oligomeric or aggregated species may result in poor reproducibility of the aggregation kinetics⁵⁸, and induce artefacts in the AFM measurements (e.g., fibrillar species will be evident at the initial stages of the aggregation), which .......

Materials

Name	Company	Catalog Number	Comments
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