title: Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations.
abstract: The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.
authors.affiliation: Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA. shea@chem.ucsb.edu.|Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA. shea@chem.ucsb.edu.
authors.forename: Joan-Emma
authors.initials: JE
authors.lastname: Shea
authors.affiliation: Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.|Department of Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: Levine
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D056004:Molecular Dynamics Simulation; D066263:Protein Aggregation, Pathological / Q000235:genetics*; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics
chemical_list: D016229:Amyloid beta-Peptides
keywords: Alzheimer’s disease; Amyloid fibrils; Intrinsically disordered proteins; Molecular dynamics simulations; Protein aggregation; Protein folding; Replica exchange molecular dynamics; Tau protein