Kim J H, Marshall A G
Department of Chemistry, Ohio State University, Columbus 43210.
Biopolymers. 1992 Sep;32(9):1263-70. doi: 10.1002/bip.360320915.
The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 A. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy.
通过能量最小化和分子动力学计算研究了巨大芽孢杆菌5S rRNA的螺旋II - III区域和螺旋IV区域的结构。计算得出螺旋II、III和IV中相邻氢键亚氨基质子之间的距离在3.5至4.5埃之间。螺旋II - III区域的整体轴是弯曲的而非笔直的。从分子动力学计算得到的原子位置来看，环B和环C中额外的沃森 - 克里克碱基对的形成并不明显。环C中的碱基堆积良好，在动力学过程中没有显著变化。螺旋III中的凸起迁移似乎不太可能；螺旋II - III区域倾向于一种构象。螺旋II比螺旋III更稳定。螺旋IV中的五个碱基对足够稳定，从而确定螺旋IV由一个三核苷酸的发夹环终止。U87从环D中突出。通过分子动力学获得的巨大芽孢杆菌5S rRNA的螺旋II - III片段和螺旋IV片段的结构与从高场质子核磁共振光谱推断出的溶液结构总体一致。
