title: Hydrodynamic effects on β-amyloid (16-22) peptide aggregation.
abstract: Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ16-22 peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ16-22 peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ16-22 peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Mara
authors.initials: M
authors.lastname: Chiricotto
authors.affiliation: CNR-ISC, Institute for Complex System, Consiglio Nazionale delle Ricerche, Rome, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Melchionna
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Fabio
authors.initials: F
authors.lastname: Sterpone
mesh_terms: D000465:Algorithms; D016229:Amyloid beta-Peptides / Q000378:metabolism*; D004058:Diffusion; D017276:Friction; D057446:Hydrodynamics; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000378:metabolism*; D066263:Protein Aggregation, Pathological; D055503:Protein Multimerization; D012996:Solutions
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D012996:Solutions; C417223:amyloid beta-protein (16-22)