Fink D L, Chen R O, Noller H F, Altman R B
Section on Medical Informatics, Stanford University, California 94305-5479, USA.
RNA. 1996 Sep;2(9):851-66.
Structural models for 16S ribosomal RNA have been proposed based on combinations of crosslinking, chemical protection, shape, and phylogenetic evidence. These models have been based for the most part on independent data sets and different sets of modeling assumptions. In order to evaluate such models meaningfully, methods are required to explicitly model the spatial certainty with which individual structural components are positioned by specific data sets. In this report, we use a constraint satisfaction algorithm to explicitly assess the location of the secondary structural elements of the 16S RNA, as well as the certainty with which these elements can be positioned. The algorithm initially assumes that these helical elements can occupy any position and orientation and then systematically eliminates those positions and orientations that do not satisfy formally parameterized interpretations of structural constraints. Using a conservative interpretation of the hydroxyl radical footprinting data, the positions of the ribosomal proteins as defined by neutron diffraction studies, and the secondary structure of 16S rRNA, the location of the RNA secondary structural elements can be defined with an average precision of 25 A (ranging from 12.8 to 56.3 A). The uncertainty in individual helix positions is both heterogeneous and dependent upon the number of constraints imposed on the helix. The topology of the resulting model is consistent with previous models based on independent approaches. The result of our computation is a conservative upper bound on the possible positions of the RNA secondary structural elements allowed by this data set, and provides a suitable starting point for refinement with other sources of data or different sets of modeling assumptions.
基于交联、化学保护、形状和系统发育证据的组合，已经提出了16S核糖体RNA的结构模型。这些模型大多基于独立的数据集和不同的建模假设集。为了有意义地评估这些模型，需要一些方法来明确地对各个结构组件由特定数据集定位的空间确定性进行建模。在本报告中，我们使用一种约束满足算法来明确评估16S RNA二级结构元件的位置，以及这些元件能够被定位的确定性。该算法最初假设这些螺旋元件可以占据任何位置和方向，然后系统地消除那些不满足结构约束的形式化参数化解释的位置和方向。使用对羟基自由基足迹数据、中子衍射研究定义的核糖体蛋白位置以及16S rRNA二级结构的保守解释，可以将RNA二级结构元件的位置定义为平均精度为25埃（范围从12.8到56.3埃）。各个螺旋位置的不确定性是不均匀的，并且取决于施加在螺旋上的约束数量。所得模型的拓扑结构与基于独立方法的先前模型一致。我们的计算结果是该数据集允许的RNA二级结构元件可能位置的保守上限，并为使用其他数据源或不同建模假设集进行优化提供了合适的起点。
