Three Popular Force Fields Predict Consensus Mechanism of Amyloid β Peptide Binding to the Dimyristoylgylcerophosphocholine Bilayer

• Published in: Journal of chemical information and modeling 2020-04, Vol.60 (4), p.2282-2293
• Main Authors: Lockhart, Christopher, Smith, Amy K, Klimov, Dmitri K
• Format: Article
• Language: English
• Subjects: Amyloid beta-Peptides; Binding; Consensus; Dimyristoylphosphatidylcholine; Fatty acids; Hydrophobicity; Lipid Bilayers; Lipids; Molecular dynamics; Molecular Dynamics Simulation; Peptides; Proteins
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.0c00096

Using all-atom explicit water replica-exchange molecular dynamics simulations, we examined the impact of three popular force fields (FF) on the equilibrium binding of Aβ10–40 peptide to the dimyristoylgylcerophosphocholine (DMPC) bilayer. The comparison included CHARMM22 protein FF with CHARMM36 lipid FF (C22), CHARMM36m protein FF with CHARMM36 lipid FF (C36), and Amber14SB protein FF with Lipid14 lipid FF (A14). Analysis of Aβ10–40 binding to the DMPC bilayer in three FFs revealed a consensus binding mechanism. Its main features include (i) a stable helical structure in the bound peptide, (ii) insertion of the C-terminus and, in part, the central hydrophobic cluster into the bilayer hydrophobic core, (iii) considerable thinning of the DMPC bilayer beneath the bound peptide coupled with significant drop in bilayer density, and (iv) a strong disordering in the DMPC fatty acid tails. Although the three FFs diverge on many details concerning Aβ and bilayer conformational ensembles, these discrepancies do not offset the features of the consensus binding mechanism. We compared our findings with other FF evaluations and proposed that an agreement between C22, C36, and A14 is a consequence of a strong ordering effect created by polar–apolar interface in the lipid bilayer. By comparing the consensus Aβ binding mechanism with experimental data, we surmise that the three tested FFs largely correctly capture the interactions of Aβ peptides with the DMPC lipid bilayer.