title: Influence of pH and sequence in peptide aggregation via molecular simulation.
abstract: We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.
authors.affiliation: Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
authors.forename: Marta
authors.initials: M
authors.lastname: Enciso
authors.affiliation: Institute for Mathematics, Freie Universität Berlin, Berlin, Germany.
authors.forename: Christof
authors.initials: C
authors.lastname: Schütte
authors.affiliation: Institute for Mathematics, Freie Universität Berlin, Berlin, Germany.
authors.forename: Luigi
authors.initials: L
authors.lastname: Delle Site
mesh_terms: D000595:Amino Acid Sequence; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D066329:Protein Aggregates; D013816:Thermodynamics
chemical_list: D010455:Peptides; D066329:Protein Aggregates