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首页> 外文期刊>Biochemistry >Characteristic domain motion in the ribosome recycling factor revealed by (15)n NMR relaxation experiments and molecular dynamics simulations.
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Characteristic domain motion in the ribosome recycling factor revealed by (15)n NMR relaxation experiments and molecular dynamics simulations.

机译：（15）n NMR弛豫实验和分子动力学模拟揭示了核糖体回收因子中的特征域运动。

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摘要

The backbone dynamics of ribosome recycling factor (RRF) from Escherichia coli in water were characterized by (15)N NMR relaxation analysis and molecular dynamics (MD) simulation. RRF is composed of two domains connected by a joint region that consists of two peptide chains, such that the overall structure seems to mimic that of tRNA. MD trajectories indicated that the relative orientation of domains varies on the nanosecond time scale. We analyzed the observed (15)N T(1), T(2), and NOE using an extended model-free spectral density function in which the domain motions with a nanosecond time scale were considered. At 30 degrees C, the order parameters of slow motion () were determined to be approximately 0.9 for domain I and 0.7 for domain II, respectively. These values indicate that domain I is nearly fixed on the molecular diffusion frame, and domain II is wobbling in a cone for which the semi-angle is about 30 degrees.
机译：通过（15）N NMR弛豫分析和分子动力学（MD）模拟来表征大肠杆菌中核糖体再循环因子（RRF）的主链动力学。 RRF由通过两个肽链组成的关节区域连接的两个结构域组成，因此总体结构似乎模仿tRNA的结构。 MD轨迹表明，域的相对取向在纳秒级时标上变化。我们使用扩展的无模型谱密度函数分析了观察到的（15）N T（1），T（2）和NOE，其中考虑了具有纳秒级时标的域运动。在30摄氏度下，慢动作（）的阶次参数分别确定为对于域I和域II分别约为0.9和0.7。这些值表明结构域I几乎固定在分子扩散框架上，结构域II在圆锥中摆动，该圆锥的半角约为30度。

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