Weisz K, Shafer R H, Egan W, James T L
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446.
Biochemistry. 1994 Jan 11;33(1):354-66. doi: 10.1021/bi00167a046.
The solution structure of the DNA decamer d(CATTTGCATC)-d(GATGCAAATG), comprising the octamer motif of immunoglobulin genes, is determined by restrained molecular dynamics (rMD) simulations. The restraint data set includes interproton distances and torsion angles for the deoxyribose sugar ring which were previously obtained by a complete relaxation matrix analysis of the two-dimensional nuclear Overhauser enhancement (2D NOE) intensities and by the quantitative simulation of cross-peaks in double-quantum-filtered correlated (2QF-COSY) spectra. The influence of torsion angles and the number of experimental distance restraints on the structural refinement has been systematically examined. Omitting part of the experimental NOE-derived distances results in reduced restraint violations and lower R factors but impairs structural convergence in the rMD refinement. Eight separate restrained molecular dynamics simulations were carried out for 20 ps each, starting from either energy-minimized A- or B-DNA. Mutual atomic root-mean-square (rms) differences among the refined structures are well below 1 A and comparable to the rms fluctuations of the atoms about their average position, indicating convergence to essentially identical structures. The average refined structure was subjected to an additional 100 ps of rMD simulations and analyzed in terms of average torsion angles and helical parameters. The B-type duplex exhibits clear sequence-dependent variations in its geometry with a narrow minor groove at the T3.A3 tract and a large positive roll at the subsequent TG.CA step. This is accompanied by a noticeable bend of the global helix axis into the major groove. There is also evidence of significant flexibility of the sugar-phosphate backbone with rapid interconversion among different conformers.
包含免疫球蛋白基因八聚体基序的DNA十聚体d（CATTTGCATC）-d（GATGCAAATG）的溶液结构通过受限分子动力学（rMD）模拟确定。约束数据集包括脱氧核糖糖环的质子间距离和扭转角，这些数据先前是通过对二维核Overhauser增强（2D NOE）强度进行完整的弛豫矩阵分析以及通过双量子滤波相关（2QF-COSY）光谱中的交叉峰定量模拟获得的。系统地研究了扭转角和实验距离约束数量对结构精修的影响。省略部分实验性NOE衍生距离会导致约束违反减少和R因子降低，但会损害rMD精修中的结构收敛。从能量最小化的A-DNA或B-DNA开始，分别进行了八次单独的受限分子动力学模拟，每次模拟20皮秒。精修结构之间的相互原子均方根（rms）差异远低于1埃，与原子围绕其平均位置的均方根波动相当，表明收敛到基本相同的结构。对平均精修结构进行了额外的100皮秒rMD模拟，并根据平均扭转角和螺旋参数进行了分析。B型双链体在其几何形状上表现出明显的序列依赖性变化，在T3.A3片段处有狭窄的小沟，在随后的TG.CA步处有大的正滚动。这伴随着全局螺旋轴明显向大沟弯曲。也有证据表明糖磷酸主链具有显著的灵活性，不同构象之间能快速相互转换。
