Lustig B, Covell D G, Jernigan R L
Laboratory of Mathematical Biology, Washington Science Center, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.
J Biomol Struct Dyn. 1994 Aug;12(1):145-61. doi: 10.1080/07391102.1994.10508093.
The Phe t-RNA structure can be fit with one point per nucleotide to lattice models, and a fit for the 76 points to a face-centered cubic lattice is achieved with an RMS of 1.76 A. There are 32 chain folds possible upon these points. Because it is impossible to calculate directly all combinations of potential base pairs for these cases, an alternative is to determine low energy secondary structures and subsequently the tertiary pairs. For each lattice fold, the low energy secondary structures are generated from a list of proximal bases. From the lists of remaining possible tertiary pairs, all combinations are generated, and these include 2,365,440 allowed conformers. Among the possible types of non-native conformational variations observed is slip pairing, accompanied by a bulge, at the end of a stem. Small changes in secondary structure can result in different tertiary pairs. Other calculations, not constrained to the t-RNA shape, are presented that involve the packing of rigid stems on a flexible internal loop. For a simple cubic lattice there are 36,484,128 lattice folds for the sixteen bases enclosing the internal loop. By attaching rigid stems and accounting for their excluded volume these are reduced to only 258,979 possible configurations. The most common stacking arrangements involve the usual two pairs of stacked stems indicated in the crystal structure. The present enumerations suggest that a completely thorough exploration of three dimensional RNA structures is feasible only with prior specification of restrictions on conformational freedom, such as those given by secondary structures.
苯丙氨酸转运RNA（Phe t-RNA）结构可以将每个核苷酸对应一个点拟合到晶格模型中，76个点拟合到面心立方晶格时的均方根偏差（RMS）为1.76埃。在这些点上有32种链折叠方式。由于无法直接计算这些情况下潜在碱基对的所有组合，另一种方法是确定低能量二级结构，随后确定三级碱基对。对于每个晶格折叠，低能量二级结构由近端碱基列表生成。从剩余可能的三级碱基对列表中生成所有组合，其中包括2365440种允许的构象。在观察到的可能的非天然构象变化类型中，有一种是在茎末端的滑配对，并伴有一个凸起。二级结构的微小变化会导致不同的三级碱基对。还给出了其他不受t-RNA形状限制的计算，这些计算涉及柔性内环上刚性茎的堆积。对于简单立方晶格，围绕内环的16个碱基有36484128种晶格折叠。通过连接刚性茎并考虑它们的排除体积，这些折叠减少到只有258979种可能的构型。最常见的堆积排列方式涉及晶体结构中通常的两对堆叠茎。目前的枚举表明，只有事先对构象自由度进行限制，例如由二级结构给出的限制，才有可能对三维RNA结构进行完全彻底的探索。
