title: Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.
abstract: The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.
authors.affiliation: Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Yannick G
authors.initials: YG
authors.lastname: Spill
authors.affiliation: Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Samuela
authors.initials: S
authors.lastname: Pasquali
authors.affiliation: Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux