Morikawa S, Ogata K, Sekikawa A, Sarai A, Ishii S, Nishimura Y, Nakamura H
Protein Engineering Research Institute, Osaka, Japan.
J Biomol NMR. 1995 Nov;6(3):294-305. doi: 10.1007/BF00197810.
The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement (NOE) distance restraints. In order to determine the complex structure independent of the initial guess, we have developed two different procedures for the docking calculation using simulated annealing in four-dimensional space (4D-SA). One is a multiple-step procedure, where the protein and the DNA were first constructed independently by 4D-SA using only the individual intramolecular NOE distance restraints. Here, the initial structure of the protein was a random coil and that of the DNA was a typical B-form duplex. Then, as the starting structure for the next docking procedure, the converged protein and DNA structures were placed in random molecular orientations, separated by 50 A. The two molecules were docked by 4D-SA utilizing all the restraints, including the additional 66 intermolecular distance restraints. The second procedure comprised a single step, in which a random-cell protein and a typical B-form DNA duplex were first placed 70 A from each other. Then, using all the intramolecular and intermolecular NOE distance restraints, the complex structure was constructed by 4D-SA. Both procedures yielded the converged complex structures with similar quality and structural divergence, but the multiple-step procedure has much better convergence power than the single-step procedure. A model study of the two procedures was performed to confirm the structural quality, depending upon the number of intermolecular distance restraints, using the X-ray structure of the engrailed homeodomain-DNA complex.
通过使用一组1732个核Overhauser增强（NOE）距离约束进行距离几何计算，确定了小鼠c-Myb蛋白最小DNA结合结构域的特定DNA复合物的溶液结构。为了独立于初始猜测确定复合物结构，我们开发了两种不同的程序，用于在四维空间中使用模拟退火进行对接计算（4D-SA）。一种是多步程序，其中首先仅使用单个分子内NOE距离约束通过4D-SA独立构建蛋白质和DNA。在这里，蛋白质的初始结构是无规卷曲，DNA的初始结构是典型的B型双链体。然后，作为下一个对接程序的起始结构，将收敛的蛋白质和DNA结构以随机分子取向放置，相距50埃。利用所有约束，包括额外的66个分子间距离约束，通过4D-SA对接这两个分子。第二个程序包括一个步骤，其中首先将随机细胞蛋白和典型的B型DNA双链体彼此放置70埃。然后，使用所有分子内和分子间NOE距离约束，通过4D-SA构建复合物结构。两种程序都产生了具有相似质量和结构差异的收敛复合物结构，但多步程序的收敛能力比单步程序好得多。使用engrailed同源结构域-DNA复合物的X射线结构，对这两种程序进行了模型研究，以根据分子间距离约束的数量确认结构质量。
