Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism

doi:10.1016/j.jmb.2009.09.010

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	Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism
	Huang, Yongqi ; Liu, Zhirong 1
刊名	JOURNAL OF MOLECULAR BIOLOGY
	2009-11-13
卷号	393 期号:5 页码:1143-1159
关键词	"fly-casting" Mechanism Intrinsically Disordered Protein Coupled Folding-binding Coarse-grained Simulation Capture Radius
ISSN号	0022-2836
DOI	10.1016/j.jmb.2009.09.010
英文摘要	Intrinsically disordered proteins (IDPs) are recognized to play important roles in many biological functions such as transcription and translation regulation, cellular signal transduction, protein phosphorylation, and molecular assemblies. The coupling of folding with binding through a "fly-casting" mechanism has been proposed to account for the fast binding kinetics of IDPs. In this article, experimental data from the literature were collated to verify the kinetic advantages of IDPs, while molecular simulations were performed to clarify the origin of the kinetic advantages. The phosphorylated KID-kinase-inducible domain interacting domain (KIX) complex was used as an example in the simulations. By modifying a coarse-grained model with a native-centric Go-like potential, we were able to continuously tune the degree of disorder of the phosphorylated KID domain and thus investigate the intrinsic role of chain flexibility in binding kinetics. The simulations show that the "fly-casting" effect is not only due to the greater capture radii of IDPs. The coupling of folding with binding of IDPs leads to a significant reduction in binding free-energy barrier. Such a reduction accelerates the binding process. Although the greater capture radius has been regarded as the main factor in promoting the binding rate of IDPs, we found that this parameter will also lead to the slower translational diffusion of IDPs when compared with ordered proteins. As a result, the capture rate of IDPs was found to be slower than that of ordered proteins. The main origin of the faster binding for IDPs are the fewer encounter times required before the formation of the final binding complex. The roles of the interchain native contacts fraction (Q(b)) and the mass-center distance (Delta R) as reaction coordinates are also discussed. (C) 2009 Elsevier Ltd. All rights reserved.
语种	英语
出版者	ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
WOS记录号	WOS:000271596500013
内容类型	期刊论文
源URL	[http://ir.iccas.ac.cn/handle/121111/67269]
专题	中国科学院化学研究所
通讯作者	Liu, Zhirong
作者单位	1.Peking Univ, Coll Chem & Mol Engn, Ctr Theoret Biol, State Key Lab Struct Chem Unstable & Stable Speci, Beijing 100871, Peoples R China 2.Peking Univ, Beijing Natl Lab Mol Sci, Beijing 100871, Peoples R China
推荐引用方式 GB/T 7714	Huang, Yongqi,Liu, Zhirong. Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism[J]. JOURNAL OF MOLECULAR BIOLOGY,2009,393(5):1143-1159.
APA	Huang, Yongqi,&Liu, Zhirong.(2009).Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism.JOURNAL OF MOLECULAR BIOLOGY,393(5),1143-1159.
MLA	Huang, Yongqi,et al."Kinetic Advantage of Intrinsically Disordered Proteins in Coupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting" Mechanism".JOURNAL OF MOLECULAR BIOLOGY 393.5(2009):1143-1159.