Allmang C, Mougel M, Westhof E, Ehresmann B, Ehresmann C
UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France.
Nucleic Acids Res. 1994 Sep 11;22(18):3708-14. doi: 10.1093/nar/22.18.3708.
Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.
核糖体蛋白S8特异性识别16S rRNA的一个螺旋且不规则的区域，该区域在进化上受到高度限制。尽管其大小有限，但该区域的确切构象仍是一个有争议的问题。在这里，我们使用化学探针分析该RNA区域突变的结构后果。这些数据，结合计算机建模和先前发表的关于蛋白质结合的数据，用于研究RNA结合位点的构象。实验数据证实了腺嘌呤A595、A640和A642在深沟中突出的模型。除了已经提出的非经典U598-U641相互作用外，该结构还通过堆积相互作用（A595和A640之间）以及涉及碱基和糖磷酸骨架的一系列氢键得以稳定。改变形成这些相互依赖相互作用能力的突变会导致局部不稳定或重组。蛋白质S8识别的特异性由深沟中不规则且扭曲的骨架以及两个突出的腺嘌呤640和642提供。第三个腺嘌呤（A595）不是直接识别位点，但必须处于突出位置。U598-U641对不应直接与蛋白质接触。
