Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

TitleLattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides
Publication TypeJournal Article
Year of Publication2016
AuthorsTran TThuy, Nguyen PH, Derreumaux P
JournalJ. Chem. Phys.
Volume144
Date Publishedmay
ISSN0021-9606
Abstract

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments A beta(16-22) and A beta(37-42) of the full length A beta(1-42) Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the A beta(16-22) dimer by fitting its equilibrium parallel and anti-parallel beta-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of A beta(16-22) and the dimer and trimer of A beta(37-42). Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the A beta(16-22) decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the A beta(37-42) decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. Published by AIP Publishing.

DOI10.1063/1.4951739
Citation Key2016|1703