Characteristic Domain Motion in the Ribosome Recycling Factor Revealed by 15N NMR Relaxation Experiments and Molecular Dynamics Simulations

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• 作者：Takuya Yoshida ; Shinichiro Oka ; Susumu Uchiyama ; Hiroaki Nakano ; Tadayuki Kawasaki ; Tadayasu Ohkubo ; and Yuji Kobayashi
• 刊名：Biochemistry
• 出版年：2003
• 出版时间：April 15, 2003
• 年：2003
• 卷：42
• 期：14
• 页码：4101 - 4107
• 全文大小：304K
• 年卷期：v.42,no.14(April 15, 2003)
• ISSN：1520-4995

文摘

The backbone dynamics of ribosome recycling factor (RRF) from Escherichia coli in waterwere characterized by ¹⁵N NMR relaxation analysis and molecular dynamics (MD) simulation. RRF iscomposed of two domains connected by a joint region that consists of two peptide chains, such that theoverall structure seems to mimic that of tRNA. MD trajectories indicated that the relative orientation ofdomains varies on the nanosecond time scale. We analyzed the observed ¹⁵N T₁, T₂, and NOE using anextended model-free spectral density function in which the domain motions with a nanosecond time scalewere considered. At 30 C, the order parameters of slow motion (27191ye10001.gif">) were determined to beapproximately 0.9 for domain I and 0.7 for domain II, respectively. These values indicate that domain Iis nearly fixed on the molecular diffusion frame, and domain II is wobbling in a cone for which thesemi-angle is about 30.