标题： RNA结构的尺寸、形状和柔性 显示英文标题

标题： Size, shape, and flexibility of RNA structures

摘要： 确定RNA分子的尺寸和柔性对于理解折叠结构中的包装性质以及阐明RNA与DNA或蛋白质之间的相互作用非常重要。 使用蛋白质数据银行中RNA结构的坐标，我们发现折叠RNA结构的尺寸，通过回转半径测量，$R_G$，遵循Flory标度定律，即$R_G =5.5 N^{1/3}$ \AA ，其中N是核苷酸的数量。 RNA分子的形状由非球性$\Delta$和形状$S$参数表征，这些参数是通过惯性张量的特征值计算得到的。 从$\Delta$的分布可以看出，大量折叠的 RNA 结构是不对称的，$S$值的分布表明 RNA 分子是杆状的（$S>0$）。折叠结构的柔韧性由持久长度$l_p$来表征。通过将距离分布函数$P(r)$拟合到蠕虫链模型，我们提取了持久长度$l_p$。 我们发现$l_p\approx 1.5 N^{0.33}$ \AA 。 $l_p$对$N$的依赖表明，随着 RNA 尺寸的增大，螺旋的平均长度应该会增加。 我们还从$R_G$、$\Delta$、$S$和$l_p$的角度分析了核糖体（30S、50S 和 70S）结构中的填充情况。 与大多数 RNA 分子相比，70S 和 50S 亚基更接近球形。 50S 的球形是由于存在比 30S 亚基多得多的小螺旋，这些小螺旋通过膨出和环连接在一起。 完整 70S 核糖体和组成它的颗粒形状的比较表明，单个分子的折叠可能在组装之前发生。 显示英文摘要

摘要： Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of RNA in the Protein Data Bank we find that the size of the folded RNA structures, measured using the radius of gyration, $R_G$, follows the Flory scaling law, namely, $R_G =5.5 N^{1/3}$ \AA where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity $\Delta$ and the shape $S$ parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of $\Delta$, we find that a large fraction of folded RNA structures are aspherical and the distribution of $S$ values shows that RNA molecules are prolate ($S>0$). The flexibility of folded structures is characterized by the persistence length $l_p$. By fitting the distance distribution function $P(r)$ to the worm-like chain model we extracted the persistence length $l_p$. We find that $l_p\approx 1.5 N^{0.33}$ \AA. The dependence of $l_p$ on $N$ implies the average length of helices should increases as the size of RNA grows. We also analyze packing in the structures of ribosomes (30S, 50S, and 70S) in terms of $R_G$, $\Delta$, $S$, and $l_p$. The 70S and the 50S subunits are more spherical compared to most RNA molecules. The globularity in 50S is due to the presence of an unusually large number (compared to 30S subunit) of small helices that are stitched together by bulges and loops. Comparison of the shapes of the intact 70S ribosome and the constituent particles suggests that folding of the individual molecules might occur prior to assembly.