Molecular dynamics simulations of amyloid fibrils: an in silico approach

Wei Ye, Wei Wang, Cheng Jiang, Qingfen Yu and Haifeng Chen

State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China  

Acta Biochim Biophys Sin 2013, 45: 503–508; doi: 10.1093/abbs/gmt026

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.

Applications of MD simulations on different amyloid fibrils

全文: http://abbs.oxfordjournals.org/content/45/6/503.full 

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