Strahs Daniel, Barash Danny, Qian Xiaoliang, Schlick Tamar
Department of Chemistry, New York University and Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA.
Biopolymers. 2003 Jun;69(2):216-43. doi: 10.1002/bip.10409.
The TATA element is a well-known example of a DNA promoter sequence recognized by the TATA box binding protein (TBP) through its intrinsic motion and deformability. Although TBP recognizes the TATA element octamer unusually (through the minor groove, which lacks the distinctive features of the major groove), single base-pair replacements alter transcriptional activity. Recent crystallographic experiments have suggested that TATA/TBP complexes differing by a single base pair retain substantial structural similarity despite their functional differences in activating transcription. To investigate the subtle role of sequence-dependent motion within the TATA element and certain aspects of its effect on assembly of the transcriptional complex, we examine 5-ns dynamics trajectories of 13 variant TATA/TBP complexes differing from each other by a single base pair. They include the wild-type (WT) adenovirus 2 major late promoter (AdMLP) TATA element, TATAAAAG (the octamer specifies positions -31 to -24 with respect to the transcription initiation site), and the variants A31 (i.e., AATAAAAG), T30, A29, C29, G28, T28, T27, G26, T26, C25, T25, and T24. Our simulated TATA/TBP complexes develop sequence-dependent structure and motion trends that may lead to favorable orientations for high-activity variants (with respect to binding TFIIA, TFIIB, and other transcription factors), while conversely, accelerate dissociation of low-activity TATA/TBP complexes. The motions that promote favorable geometries for preinitiation complexes include small rotations between TBP's N- and C-terminal domains, sense strand DNA backbone "slithering," and rotations in TBP's H2 and H2' helices. Low-activity variants tend to translate the H1 and H1' helices and withdraw the intercalating phenylalanines. These cumulative DNA and protein motions lead to a spatial spread of complex orientations up to 4 A; this is associated with an overall bend of the variant TATA/TBP complexes that spans 93 degrees to 110 degrees (107 degrees for the crystal reference). Taken together, our analyses imply larger differences when these local structural and bending changes are extended to longer DNA (upstream and downstream) and suggest that specific local TATA/TBP motions (e.g., shifts in TBP helices and TATA bases and backbone) play a role in modulating the formation and maintenance of the transcription initiation complex.
TATA元件是一种著名的DNA启动子序列实例，它可被TATA框结合蛋白（TBP）通过其内在运动和可变形性识别。尽管TBP以不同寻常的方式（通过缺乏大沟独特特征的小沟）识别TATA元件八聚体，但单碱基对替换会改变转录活性。最近的晶体学实验表明，相差一个碱基对的TATA/TBP复合物尽管在激活转录方面存在功能差异，但仍保留了大量结构相似性。为了研究TATA元件内序列依赖性运动的微妙作用及其对转录复合物组装影响的某些方面，我们研究了13种相差一个碱基对的变体TATA/TBP复合物的5纳秒动力学轨迹。它们包括野生型（WT）腺病毒2主要晚期启动子（AdMLP）TATA元件TATAAAAG（八聚体相对于转录起始位点指定位置-31至-24），以及变体A31（即AATAAAAG）、T30、A29、C29、G28、T28、T27、G26、T26、C25、T25和T24。我们模拟的TATA/TBP复合物呈现出序列依赖性结构和运动趋势，这可能导致高活性变体（相对于结合TFIIA、TFIIB和其他转录因子）形成有利的取向，而相反，会加速低活性TATA/TBP复合物的解离。促进起始前复合物形成有利几何形状的运动包括TBP的N端和C端结构域之间的小旋转、有义链DNA主链的“滑动”以及TBP的H2和H2'螺旋中的旋转。低活性变体倾向于平移H1和H1'螺旋并撤回插入的苯丙氨酸。这些累积的DNA和蛋白质运动导致复合物取向的空间扩散高达4埃；这与变体TATA/TBP复合物的整体弯曲相关，弯曲范围为93度至110度（晶体参考为107度）。综合来看，我们的分析表明，当这些局部结构和弯曲变化扩展到更长的DNA（上游和下游）时，差异会更大，并表明特定的局部TATA/TBP运动（例如，TBP螺旋、TATA碱基和主链的移动）在调节转录起始复合物的形成和维持中起作用。
