Lillemoen J, Hoffman D W
Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
J Mol Biol. 1998 Aug 21;281(3):539-51. doi: 10.1006/jmbi.1998.1946.
The dynamic properties of ribosomal protein L9 from Bacillus stearothermophilus were investigated in solution using an analysis of nitrogen-15 longitudinal and transverse relaxation rates and amide nitrogen-proton nuclear Overhauser effects. The relaxation rates of the amide nitrogen nuclei were found to be correlated with the angle between the amide nitrogen-proton bond vectors and the long axis of the protein. This directional dependence of the nuclear relaxation rates is consistent with the protein having a highly elongated shape in solution, consistent with that observed in previous X-ray crystallographic studies of the crystalline form. Analysis of the nuclear relaxation data shows that the solvent-exposed nine-turn alpha helix connecting the two domains has a relatively high degree of order, in contrast to the connecting helix in the similarly shaped, but functionally different, calmodulin protein. The rotational correlation times associated with the amide nitrogen atoms of the N-terminal domain are on average slightly shorter than those of the C-terminal domain and connecting helix, providing evidence that the N-terminal domain exhibits some degree of independence in tumbling, in addition to other fast internal motions. The putative RNA-binding surfaces in each of the protein domains are characterized by relatively low order parameters, indicating that these are the most flexible regions of the molecule. Overall, the picture of the internal dynamics provided by nuclear relaxation measurements is similar to that obtained from a detailed study of amide proton exchange rates, but differs markedly from the picture provided by crystallographic temperature factors. The present study describes a molecule with unusual and complex dynamic properties, and supports a model where the protein functions as a "molecular strut" within the ribosome.
利用氮-15纵向和横向弛豫速率以及酰胺氮-质子核Overhauser效应分析，对嗜热脂肪芽孢杆菌核糖体蛋白L9在溶液中的动力学性质进行了研究。发现酰胺氮核的弛豫速率与酰胺氮-质子键向量和蛋白质长轴之间的夹角相关。核弛豫速率的这种方向依赖性与该蛋白质在溶液中具有高度细长的形状一致，这与先前对晶体形式的X射线晶体学研究中观察到的情况相符。对核弛豫数据的分析表明，连接两个结构域的溶剂暴露的九圈α螺旋具有相对较高的有序度，这与形状相似但功能不同的钙调蛋白中的连接螺旋相反。与N端结构域的酰胺氮原子相关的旋转相关时间平均略短于C端结构域和连接螺旋的旋转相关时间，这表明N端结构域除了其他快速内部运动外，在翻滚中还表现出一定程度的独立性。每个蛋白质结构域中假定的RNA结合表面的特征是相对较低的序参数，表明这些是分子中最灵活的区域。总体而言，核弛豫测量提供的内部动力学情况与通过对酰胺质子交换速率的详细研究获得的情况相似，但与晶体学温度因子提供的情况明显不同。本研究描述了一种具有异常和复杂动力学性质的分子，并支持该蛋白质在核糖体中作为“分子支柱”发挥作用的模型。
