Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer

Abstract

To propose new mechanism-based therapeutics for Alzheimer’s disease (AD), it is crucial to study the kinetics and oligomerization/aggregation mechanisms of the hallmark tau proteins, which have various isoforms and are intrinsically disordered. In this study, multiple all-atom (AA) and coarse-grained (CG) force fields (FFs) have been benchmarked on molecular dynamics (MD) simulations of K18 tau (M243–E372), which is a truncated form (130 residues) of full-length tau (441 residues). FF19SB is first excluded because the dynamics are too slow, and the conformations are too stable. All other benchmarked AAFFs (Charmm36m, FF14SB, Gromos54A7, and OPLS-AA) and CGFFs (Martini3 and Sirah2.0) exhibit a trend of shrinking K18 tau into compact structures with the radius of gyration (ROG) around 2.0 nm, which is much smaller than the experimental value of 3.8 nm, within 200 ns of AA-MD or 2000 ns of CG-MD. Gromos54A7, OPLS-AA, and Martini3 shrink much faster than the other FFs. To perform meaningful postanalysis of various properties, we propose a strategy of selecting snapshots with 2.5 < ROG < 4.5 nm, instead of using all sampled snapshots. The calculated chemical shifts of all C, CA, and CB atoms have very good and close root-mean-square error (RMSE) values, while Charmm36m and Sirah2.0 exhibit better chemical shifts of N than other FFs. Comparing the calculated distributions of the distance between the CA atoms of CYS291 and CYS322 with the results of the FRET experiment demonstrates that Charmm36m is a perfect match with the experiment while other FFs exhibit limitations. In summary, Charmm36m is recommended as the best AAFF, and Sirah2.0 is recommended as an excellent CGFF for simulating tau K18.