Miaskiewicz K, Ornstein R L
Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA.
J Biomol Struct Dyn. 1996 Feb;13(4):593-600. doi: 10.1080/07391102.1996.10508872.
TATA-box binding protein (TBP) in a monomeric form and the complexes it forms with DNA have been elucidated with molecular dynamics simulations. Large TBP domain motions (bend and twist) are detected in the monomer as well as in the DNA complexes; these motions can be important for TBP binding of DNA. TBP interacts with guanine bases flanking the TATA element in the simulations of the complex; these interactions may explain the preference for guanine observed at these DNA positions. Side chains of some TBP residues at the binding interface display significant dynamic flexibility that results in 'flip-flop' contacts involving multiple base pairs of the DNA. We discuss the possible functional significance of these observations.
已通过分子动力学模拟阐明了单体形式的TATA框结合蛋白（TBP）及其与DNA形成的复合物。在单体以及DNA复合物中均检测到TBP结构域的大幅度运动（弯曲和扭转）；这些运动可能对TBP与DNA的结合很重要。在复合物模拟中，TBP与TATA元件侧翼的鸟嘌呤碱基相互作用；这些相互作用可能解释了在这些DNA位置观察到的对鸟嘌呤的偏好。结合界面处一些TBP残基的侧链表现出显著的动态灵活性，导致涉及DNA多个碱基对的“翻转”接触。我们讨论了这些观察结果可能的功能意义。
