Effects of force fields on the conformational and dynamic properties of amyloid [beta](1-40) dimer explored by replica exchange molecular dynamics simulations

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2018-03, Vol.86 (3), p.279
• Main Authors: Watts, Charles R, Gregory, Andrew, Frisbie, Cole, Lovas, Sándor
• Format: Article
• Language: English
• Subjects: Amber; Collision dynamics; Cores; Dimers; Dynamic structural analysis; Friction; Hydrophobicity; Molecular dynamics; NMR; Nuclear magnetic resonance; Oligomers; Peptides; Random coil; Simulation
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25439

The conformational space and structural ensembles of amyloid beta (A[beta]) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the A[beta](1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8±6.4%) and CHARMM36 (2.7±4.2%), tend to overestimate the [alpha]-helical content compared to experimental CD (5.3±5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3±12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of [beta]-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected [beta]-sheet-turn-[beta]-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.