Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations

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• 作者：Trang Nhu Do ; Wing-Yiu Choy ; Mikko Karttunen
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2016
• 出版时间：January 12, 2016
• 年：2016
• 卷：12
• 期：1
• 页码：395-404
• 全文大小：676K
• ISSN：1549-9626

文摘

Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch’s IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA’s lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding–binding, and confirms the essential role of linear motifs in IDP binding.