Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder

Abstract

Recent evidence suggests that amyloidogenic oligomers may be the toxic species in cell cultures. Thus, it is crucial to understand their structure and oligomerization mechanism in atomistic detail. By employing tens of fast central processing units and an advanced phase-space sampling algorithm, parallel-tempering molecular dynamics, we have explored the energy landscape of amyloidogenic peptide oligomerization in explicit water. A pentapeptide, DFNKF, derived from human calcitonin and its mutant, DFAKF, was simulated with a total simulation time of Ϸ500 ns. The detailed oligomerization process of a DFNKF parallel ␤-sheet formation at 300 K has been characterized. The assembly of a parallel ␤-sheet from the amorphous state mainly occurs via a ''bottleneck'' channel where the interstrand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking include both backbone and side-chain hydrogen bonds. The Asn-Asn interactions work like ''glue'' by sticking the DFNKF strands together and assist the ''on-pathway'' oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder commonly found in globular ␤-helix proteins. A control run shows that when Asn is mutated to Ala, the stability and population of the DFAKF parallel ␤-sheet is decreased. Furthermore, our in vitro mutagenesis experiments show that the ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with the simulations. Knowledge of the energy landscape of oligomerization may provide hints for rational drug design, preventing amyloid-associated diseases.amyloid oligomerization ͉ bottleneck channel ͉ ␤-helix ͉ human calcitonin ͉ mutagenesis P roteins fold in vivo into their unique 3D structures to perform their biological functions. Yet, under certain conditions, proteins can misfold and aggregate, leading to the malfunctioning of the organism (1). Amyloid fibrosis is one such example, involving severe diseases such as Alzheimer's disease, Prion disorder, and Parkinson's disease (1). Although amyloidogenic diseases are characterized by the deposition of insoluble amyloid fibrils, recent evidence suggests that amyloid oligomers and protofibrils may actually be the toxic agents (2, 3). The increasing appreciation of the importance of the toxic oligomers in the pathological process has attracted considerable attention, focusing not only on their structures but also on the details of their oligomerization mechanism (4-6).X-ray diffraction data indicate that amyloid fibrils from peptides of unrelated origins have a similar cross-␤-fibril organization (7). Also, amyloidogenic proteins do not share sequence or structural homology. The noncrystallinity and insolubility of amyloid fibrils complicate the determination of their structures in atomic detail by conventional methods, such as x-ray crystallography and solution NMR. Nevertheless, the mechanisms of formation and the structure of amyloid fibrils are starting to be revealed by a number of experimental (8-10) and molecularmodeling methods (...

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