Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic β2-microglobulin variant

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 108; no. 4; pp. 1314 - 1319
• Main Authors: Domanska, Katarzyna, Vanderhaegen, Saskia, Srinivasan, Vasundara, Pardon, Els, Dupeux, Florine, Marquez, Jose A, Giorgetti, Sofia, Stoppini, Monica, Wyns, Lode, Bellotti, Vittorio, Steyaert, Jan
• Format: Journal Article
• Language: English
• Published: National Academy of Sciences 25.01.2011; National Acad Sciences
• Subjects: Aggregation; Amyloids; Antibodies; Biological Sciences; Cell aggregates; Crystal structure; Dimers; Monomers; Oligomers; Proteins; Solar fibrils
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1008560108

Atomic-level structural investigation of the key conformational intermediates of amyloidogenesis remains a challenge. Here we demonstrate the utility of nanobodies to trap and characterize intermediates of β2-microglobulin (β2m) amyloidogenesis by X-ray crystallography. For this purpose, we selected five single domain antibodies that block the fibrillogenesis of a proteolytic amyloidogenic fragment of β2m (ΔN6β2m). The crystal structure of ΔN6β2m in complex with one of these nanobodies (Nb24) identifies domain swapping as a plausible mechanism of self-association of this amyloidogenic protein. In the swapped dimer, two extended hinge loops—corresponding to the heptapetide NHVTLSQ that forms amyloid in isolation—are unmasked and fold into a new two-stranded antiparallel β-sheet. The β-strands of this sheet are prone to self-associate and stack perpendicular to the direction of the strands to build large intermolecular β-sheets that run parallel to the axis of growing oligomers, providing an elongation mechanism by self-templated growth.