title: Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.
abstract: Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid β(1-40) (Aβ(1-40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was -93.56 ± 6.341 kJ mol-1. Prevalence of random coil conformations was found for both chains with the exceptions of increased β-sheet content from residues 16-21 and 29-32 of chain A and residues 15-21 and 30-33 of chain B with β-turn/β-bend conformations in both chains from residues 1-16, 21-29 of chain A, 1-16, and 21-29 of chain B. There is a mixed β-turn/β-sheet region from residues 33-38 of both chains. Analysis of intra- and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel β-sheet configuration with contacts between residues 17-21 of chain A with residues 17-21 and 31-36 of chain B as well as residues 31-36 of chain A with residues 17-21 and 31-36 of chain B. Based on dihedral principal component analysis, the antiparallel β-sheet-loop-β-sheet conformational motif is favored for many low energy sampled conformations. Our results show that Aβ(1-40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C-terminal hydrophobic cores with the expected β-sheet-loop-β-sheet conformational motif. Proteins 2017; 85:1024-1045. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota, 55905.|Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601.
authors.forename: Charles R
authors.initials: CR
authors.lastname: Watts
authors.affiliation: Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Gregory
authors.affiliation: Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin, 54601.|Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, 61718.
authors.forename: Cole P
authors.initials: CP
authors.lastname: Frisbie
authors.affiliation: Department of Biomedical Sciences, Creighton University, Omaha, Nebraska, 61718.
authors.forename: Sándor
authors.identifier: 0000-0002-5089-5186
authors.initials: S
authors.lastname: Lovas
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry*; D001665:Binding Sites; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D054802:Molecular Imprinting; D010446:Peptide Fragments / Q000737:chemistry*; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D055503:Protein Multimerization; D013696:Temperature; D013816:Thermodynamics
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; C078592:amyloid beta-protein (1-40)
keywords: REMD simulation; amyloid β; dimerization; inherently disordered peptide; loosely packed antiparallel β-sheet dimer