Afsheen Shabaz, SoCoBio DTP student, is excited to share her first publication from her doctoral research. Afsheen collaborated with members of Dr Wei-Feng Xue’s group at the University of Kent including SoCoBio DTP student Claudia Chitty.
Accumulation of a range of amyloid structures such as those formed from the amyloid-beta plaques and tau neurofibrillary tangles in Alzheimer’s disease, play a crucial role in the pathology of neurodegenerative and metabolic diseases.
Unlike globular proteins, which usually result from the folding of polypeptide chains into a single well-defined 3D-structure, amyloid-forming peptides and proteins of the same sequence in the same disease state can assemble into a diverse range of distinct structures due to structural polymorphism. Moreover, individual polymorph structures from the same sequence can be associated with different disease states.
The influence of physiological and environmental conditions on amyloid polymorphism, widely observed in vitro and in patient-derived samples, remains poorly understood, mainly due to the dearth of structural information at single-fibril level. It is of paramount importance to develop an experimental approach that allows structural analysis of individual amyloid filaments to identify different polymorphs, characterise whole amyloid populations and establish their impact on amyloid aggregation and function in disease progression.
Atomic Force Microscopy (AFM) has emerged as a powerful technique to investigate the structural polymorphism of individual particles at nanometre resolution. It allows the extraction of independent structural data from individual fibrils within complex, heterogeneous and polymorphic amyloid populations, in contrast to other structure-based techniques such as cryo-EM which offers averaged structural analysis from hundreds of thousands of images.
Here, we present an in-depth step by step method for analysis of individual amyloid fibril structures from single images. We combined AFM imaging with Contact-Point Reconstruction AFM (CPR-AFM) image analysis by employing Trace_y, a software that enables 3D reconstruction of helical structures on AFM images. Our protocol provides a powerful complementary procedure to resolve structural details of individual amyloid particles within heterogeneous populations, without cross-particle averaging. The protocol and method described here are broadly applicable to 3D reconstruction of various amyloid structures and helical filaments.
By enabling detailed structural analysis of amyloid fibrils at single filament level, CPR-AFM offers an exciting opportunity towards development of improved diagnostic tools, amyloid related disease monitoring approaches, and designing of targeted polymorph specific therapeutics.
Read the full publication in Methods in Enzymology, 2026