Harris M E, Nolan J M, Malhotra A, Brown J W, Harvey S C, Pace N R
Department of Biology, Indiana University, Bloomington 47405.
EMBO J. 1994 Sep 1;13(17):3953-63. doi: 10.1002/j.1460-2075.1994.tb06711.x.
Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well established, but comparatively little is understood about its 3-D structure. In this analysis, orientation and distance constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. A molecular mechanics-based RNA structure refinement protocol was used to incorporate the distance constraints indicated by crosslinking, along with the known secondary structure of RNase P RNA and the tertiary structure of tRNA, into molecular models. Seven different structures that satisfy the constraints equally well were generated and compared by superposition to estimate helix positions and orientations. Manual refinement within the range of conformations indicated by the molecular mechanics analysis was used to derive a model of RNase P RNA with bound substrate pre-tRNA that is consistent with the crosslinking results and the available phylogenetic comparisons.
细菌核糖核酸酶P（RNase P）是一种参与tRNA成熟的内切核酸酶，是一种含有催化RNA的核糖核蛋白。这种核酶的二级结构已得到充分确立，但对其三维结构的了解相对较少。在本分析中，通过分子内和分子间交联实验确定了大肠杆菌RNase P RNA-前体tRNA复合物内各元件之间的方向和距离限制。基于分子力学的RNA结构优化方案被用于将交联所指示的距离限制，连同RNase P RNA的已知二级结构和tRNA的三级结构，纳入分子模型。生成了七个同样很好满足这些限制的不同结构，并通过叠加进行比较以估计螺旋位置和方向。在分子力学分析所指示的构象范围内进行人工优化，以推导与交联结果和现有系统发育比较一致的、结合有底物前体tRNA的RNase P RNA模型。
