Open AccessMolecular dynamics simulations of amyloid fibrils: an <italic>in silico</italic> approach
Author(s) -
Yaguang Wei,
Wei Wang,
Cheng Jiang,
Qingfen Yu,
Haifeng Chen
Publication year - 2013
Publication title -
acta biochimica et biophysica sinica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.771
H-Index - 57
eISSN - 1745-7270
pISSN - 1672-9145
DOI - 10.1093/abbs/gmt026
Subject(s) - in silico , amyloid fibril , amyloid (mycology) , molecular dynamics , fibril , mechanism (biology) , prion protein , computational biology , protein aggregation , chemistry , amyloid β , biophysics , biology , medicine , biochemistry , disease , gene , physics , inorganic chemistry , computational chemistry , quantum mechanics
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.