title: Molecular dynamics simulations of amyloid fibrils: an in silico approach.
abstract: Amyloid fibrils play causal roles in the pathogenesis of amyloid-related degenerative diseases such as Alzheimer's disease, type II diabetes mellitus, and the prion-related transmissible spongiform encephalopathies. The mechanism of fibril formation and protein aggregation is still hotly debated and remains an important open question in order to develop therapeutic method of these diseases. However, traditional molecular biological and crystallographic experiments could hardly observe atomic details and aggregation process. Molecular dynamics (MD) simulations could provide explanations for experimental results and detailed pathway of protein aggregation. In this review, we focus on the applications of MD simulations on several amyloidogenic protein systems. Furthermore, MD simulations could help us to understand the mechanism of amyloid aggregation and how to design the inhibitors.
authors.affiliation: State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ye
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Cheng
authors.initials: C
authors.lastname: Jiang
authors.forename: Qingfen
authors.initials: Q
authors.lastname: Yu
authors.forename: Haifeng
authors.initials: H
authors.lastname: Chen
mesh_terms: D000544:Alzheimer Disease / Q000378:metabolism; D000682:Amyloid / Q000737:chemistry*; D000818:Animals; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017096:Prion Diseases / Q000378:metabolism
chemical_list: D000682:Amyloid
keywords: MD simulation; amyloid fibrils; prion; protein aggregation