Molecular insights into DNAJB6 chaperone interactions with Alzheimer’s amyloid-beta peptide

Methods

GROMACS was used to perform molecular dynamics simulations of structural models of DNAJB6 in complex with amyloid-beta 42 oligomers. Its role was to test whether predicted binding arrangements remain stable over time and to enable controlled comparisons between the normal chaperone, sequence variants, domain-deletion constructs, and oligomers of different sizes. The trajectories were analysed at several complementary levels. Contact maps identified which regions of DNAJB6 remained in direct proximity to the peptide assembly. Clustered representative conformations described local rearrangements of the linker and the bound oligomer. Hydrogen-bond occupancy measurements quantified persistent polar interactions, while hydrogen-bond connectivity analysis examined how stabilizing interactions form continuous links between domains and client peptides. Interaction-energy and residue-wise analyses were used to distinguish contributions from the linker and the carboxyl-terminal domain.

Results

The first analysis route compared DNAJB6 domain combinations and the normal and mutated chaperone forms in complexes with amyloid-beta 42. Stepwise constructs comprised the carboxyl-terminal domain alone, this domain with the serine/threonine-rich linker segment, and an extended form also containing the glycine/phenylalanine-rich segment. Constructs containing the linker retained substantially stronger interactions than the carboxyl-terminal domain alone. The serine/threonine-rich segment was the principal interaction region: it showed stronger favourable interaction contributions, more persistent hydrogen bonds and more extensive contact patterns with the oligomer than the other tested regions. In the serine/threonine-to-alanine variant, the linker adopted a collapsed or displaced arrangement rather than enclosing the amyloid-beta assembly, accompanied by weakened contacts and loss of stable wrapping. The second route compared complexes containing monomeric, dimeric, trimeric, tetrameric and hexameric amyloid-beta 42. The tetramer was most effectively accommodated by the linker; smaller assemblies provided insufficient surface for complete enclosure, whereas the hexamer was too large to be fully covered. As a later extension, charged sugar simulations with amyloid-beta 28 were analysed. Their contact maps identified preferential binding to a histidine-containing peptide region, indicating a specific interaction capable of influencing aggregation.

Discussion

The results support a mechanism in which DNAJB6 captures amyloid-beta 42 oligomers primarily through its dynamic linker. The carboxyl-terminal domain provides an auxiliary recognition surface, but its interaction alone is insufficient to produce the stable enclosure observed when the linker is present. In particular, the serine/threonine-rich linker segment contributes the strongest binding network and permits the chaperone to wrap around a client of suitable size. This interpretation also accounts for the selectivity toward the tetramer: it presents an assembly large enough to engage the linker extensively, yet sufficiently compact to be enclosed. Mutation-induced collapse of the linker removes this geometric and interaction advantage, thereby weakening client capture. These findings define experimentally testable targets, including linker substitutions that should alter oligomer capture and measurements designed to distinguish stable binding to tetramers from weaker association with smaller or larger assemblies.

Additional Project Information

DFG classification: 302-03 Chemical Solid State and Surface Research, Theory and Modelling
Software: Gromacs
Cluster: CLAIX