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High-Resolution Structures of the Amyloid-β 1–42 Dimers from the Comparison of Four Atomistic Force Fields

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† Department of Physics, North Carolina State University, Raleigh, North Carolina 27695−8202, United States
‡ Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
*(P.D.) E-mail: [email protected]. Telephone: 33 1 58 41 51 72.
Cite this: J. Phys. Chem. B 2017, 121, 24, 5977–5987
Publication Date (Web):May 24, 2017
https://doi.org/10.1021/acs.jpcb.7b04689
Copyright © 2017 American Chemical Society
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    Abstract

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    The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer’s disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17–21 and 30–36 varies between 1.5% and 13%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key finding, irrespective of the force field, is that the dimer is stabilized by nonspecific interactions, explaining therefore its possible transient binding to multiple cellular partners and, in part, its toxicity.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcb.7b04689.

    • Tables S1 and S2 characterize the single-molecule and overall states of the dimer. Figures S1 and S2 are related to the convergence of the REMD simulations. Figures S3 and S4 show differences in the salt-bridge and interpeptide side-chain side-chain populations. Figure S5 shows representative structures of the 10 single-molecule states of Aβ42 dimer obtained using the four force fields. (PDF)

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