A Model of Interdomain Mobility in a Multidomain Protein
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- 作者：Yaroslav E. Ryabov ; David Fushman
- 刊名：Journal of the American Chemical Society
- 出版年：2007
- 出版时间：March 21, 2007
- 年：2007
- 卷：129
- 期：11
- 页码：3315 - 3327
- 全文大小：405K
- 年卷期：v.129,no.11(March 21, 2007)
- ISSN：1520-5126
文摘
Domain mobility plays an essential role in the biological function of multidomain systems. Thecharacteristic times of domain motions fall into the interval from nano- to milliseconds, amenable to NMRstudies. Proper analysis of NMR relaxation data for these systems in solution has to account for interdomainmotions, in addition to the overall tumbling and local intradomain dynamics. Here we propose a model ofinterdomain mobility in a multidomain protein, which considers domain reorientations as exchange/interconversion between two distinct conformational states of the molecule, combined with fully anisotropicoverall tumbling. Analysis of 15N-relaxation data for Lys48-linked diubiquitin at pH 4.5 and 6.8 showed thatthis model adequately fits the experimental data and allows characterization of both structural and motionalproperties of diubiquitin, thus providing information about the relative orientation of ubiquitin domains inboth interconverting states. The analysis revealed that the two domains reorient on a time scale of 9-30ns, with the amplitudes sufficient for allowing a protein ligand access to the binding sites sequestered atthe interface in the closed conformation. The analysis of a possible mechanism controlling the equilibriumbetween the interconverting states in diubiquitin points toward protonation of His68, which results in threedifferent charged states of the molecule, with zero, +e, and +2e net charge. Only two of the three statesare noticeably populated at pH 4.5 or 6.8, which assures applicability of the two-state model to diubiquitinat these conditions. We also compare our model with the "extended model-free" approach and discusspossible future developments of the model.