Kurkcuoglu Ozge, Kurkcuoglu Zeynep, Doruker Pemra, Jernigan Robert L
Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey.
Proteins. 2009 Jun;75(4):837-45. doi: 10.1002/prot.22292.
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 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.
利用计算效率高的弹性网络模型和简正模式分析，研究了新生多肽出口通道的集体动力学。分别考虑计算得到的简正模式，并将其与不同系数进行线性组合，以模拟模式之间的相位角，从而追踪通道壁残基的机械运动。低频波动表明通道沿三个不同区域——入口、颈部和出口——每个区域具有明显不同的结构域运动。一般来说，入口区域的内衬沿出口方向移动，出口区域的运动明显更大，但方向垂直，而受限的颈部区域有旋转运动。特别是位于通道最窄和机械关键区域的核糖体蛋白L4和L22的普遍保守延伸通常经历反相关或非相关运动，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，不受通道中肽链存在的影响。
