Wibowo Fajar R, Rauch Christine, Trieb Michael, Wellenzohn Bernd, Liedl Klaus R
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
Biopolymers. 2004 Apr 15;73(6):668-81. doi: 10.1002/bip.20023.
Water-mediated contacts are known as an important recognition tool in trp-repressor operator systems. One of these contacts involves two conserved base pairs (G(6).C(-6) and A(5). T(-5)) and three amino acids (Lys 72, Ile 79, and Ala 80). To investigate the nature of these contacts, we analyzed the X-ray structure (PDB code: 1TRO) of the trp-repressor operator complex by means of molecular dynamics simulations. This X-ray structure contains two dimers that exhibit structural differences. From these two different starting structures, two 10 ns molecular dynamics simulations have been performed. Both of our simulations show an increase of water molecules in the major groove at one side of the dimer, while the other side remains unchanged compared to the X-ray structure. Though the maximum residence time of the concerned water molecules decreases with an increase of solvent at the interface, these water molecules continue to play an important role in mediating DNA-protein contacts. This is shown by new stable amino acids-DNA distances and a long water residence time compared to free DNA simulation. To maintain stability of the new contacts, the preferential water binding site on O6(G6) is extended. This extension agrees with mutation experiment data on A5 and G6, which shows different relative affinity due to mutation on these bases [A. Joachimiak, T. E. Haran, P. B. Sigler, EMBO Journal 1994, Vol. 13, No. (2) pp. 367-372]. Due to the rearrangements in the system, the phosphate of the base G6 is able to interconvert to the B(II) substate, which is not observed on the other half side of the complex. The decrease of the number of hydrogen bonds between protein and DNA backbone could be the initial step of the dissociation process of the complex, or in other words an intermediate complex conformation of the association process. Thus, we surmise that these features show the importance of water-mediated contacts in the trp-repressor operator recognition process.
在色氨酸阻遏物-操纵基因系统中，水介导的相互作用是一种重要的识别工具。其中一种相互作用涉及两个保守碱基对（G(6).C(-6)和A(5).T(-5)）以及三个氨基酸（赖氨酸72、异亮氨酸79和丙氨酸80）。为了研究这些相互作用的本质，我们通过分子动力学模拟分析了色氨酸阻遏物-操纵基因复合物的X射线结构（PDB代码：1TRO）。该X射线结构包含两个二聚体，它们呈现出结构差异。从这两个不同的起始结构出发，进行了两个10纳秒的分子动力学模拟。我们的两个模拟均显示，二聚体一侧的大沟中水分子增加，而另一侧与X射线结构相比保持不变。尽管相关水分子的最大停留时间随着界面处溶剂的增加而减少，但这些水分子在介导DNA-蛋白质相互作用中继续发挥重要作用。与游离DNA模拟相比，新的稳定氨基酸-DNA距离和较长的水停留时间证明了这一点。为了维持新相互作用的稳定性，O6(G6)上的优先水结合位点得以扩展。这种扩展与A5和G6的突变实验数据一致，该数据表明由于这些碱基的突变而具有不同的相对亲和力[A. 约阿希米亚克、T. E. 哈兰、P. B. 西格勒，《欧洲分子生物学组织杂志》1994年，第13卷，第(2)期，第367 - 372页]。由于系统中的重排，碱基G6的磷酸能够转化为B(II)亚状态，而在复合物的另一半未观察到这种情况。蛋白质与DNA主链之间氢键数量的减少可能是复合物解离过程的初始步骤，或者换句话说，是缔合过程的中间复合物构象。因此，我们推测这些特征表明了水介导的相互作用在色氨酸阻遏物-操纵基因识别过程中的重要性。
