Collective dynamics of the ribosomal tunnel revealed by elastic network modeling.
Collective dynamics of the ribosomal tunnel revealed by elastic network modeling.
复制标题
DOI：
10.1002/prot.22292
复制
发表时间：
2009-06
影响因子：
2.9
通讯作者：
Jernigan, Robert L.
中科院分区：
文献类型：
--
作者：
Kurkcuoglu, Ozge;Kurkcuoglu, Zeynep;Doruker, Pemra;Jernigan, Robert L.
采用简正波分析的弹性网络模型研究了新生多肽出口通道的集体动力学。计算出的正常模式被认为是单独的，并在线性组合与不同的系数模仿模式之间的相位角，以遵循隧道壁残留物的机械运动。低频波动表明沿隧道沿着的三个不同区域-入口、颈部和出口-每个区域具有明显不同的畴运动。通常，入口区域的衬里在出口方向上移动，出口区域具有明显更大的运动，但是在垂直方向上，而受限的颈部区域通常具有旋转运动。特别是位于隧道最西侧的核糖体蛋白L4和L22的普遍保守延伸部分，其运动通常是反向或非相关的，这可能在新生多肽门控机制中起重要作用。这些运动似乎足够稳健，以至于不受隧道中存在的肽链的影响。
The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The low frequency fluctuations indicate three distinct regions along the tunnel - the entrance, the neck and the exit – each having distinctly different domain motions. Generally the lining of the entrance region moves in the exit direction, with the exit region having significantly larger motions, but in a perpendicular direction, whereas the confined neck region generally has rotational motions. Especially the universally conserved extensions of ribosomal proteins L4 and L22 located at the narrowest and mechanistically strategic region of tunnel undergo generally anti- or non-correlated motions, which may have an important role in nascent polypeptide gating mechanism. These motions appear to be sufficiently robust so as to be unaffected by the presence of a peptide chain in the tunnel.
登录
查看更多内容
影响因子：
9.9
作者：
通讯作者：
--
影响因子：
64.5
作者：
Nakatogawa, H;Ito, K
通讯作者：
Ito, K
影响因子：
64.8
作者：
Ferbitz, L;Maier, T;Ban, N
通讯作者：
Ban, N
影响因子：
4.6
作者：
Kurkcuoglu, O;Jernigan, RL;Doruker, P
通讯作者：
Doruker, P
影响因子：
64.8
作者：
MILLIGAN, RA;UNWIN, PNT
通讯作者：
UNWIN, PNT