Benchmarking implicit solvent folding simulations of the amyloid β(10-35) fragment

A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (A beta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric A beta(10-35) using all-atom Langevin dynamics (LD) simulations, since A beta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIMP water model) which is similar to 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for A beta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S-2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of A beta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. A beta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand - loop- strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.