Bonhoeffer S, McCaskill J S, Stadler P F, Schuster P
Institut für Theoretische Chemie, Universität Wien, Austria.
Eur Biophys J. 1993;22(1):13-24. doi: 10.1007/BF00205808.
Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest, in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced and pair correlations at the level of the structures themselves are computed. Just as with landscapes based on most stable secondary structure prediction, the landscapes defined on the full biophysical GCAU alphabet are much smoother than the landscapes restricted to pure GC sequences and the correlation lengths are almost constant fractions of the chain lengths. Correlation functions for multi-structure landscape exhibit an increased correlation length, especially near the melting temperature. However, the main effect on evolution is rather an effective increase in sampling for finite populations where each sequence explores multiple structures.
详细研究了通过配分函数算法（麦卡斯基尔，1990年）获得的RNA折叠景观的统计特性。将自由能的成对相关性作为汉明距离的函数，用作衡量景观崎岖程度的指标。与传统的最小自由能方法相比，配分函数的计算包含了作为温度函数的整个二级结构集合的信息，并为所有感兴趣的热力学量打开了大门。引入了结构集合的度量距离，并计算了结构本身层面的成对相关性。正如基于最稳定二级结构预测的景观一样，在完整的生物物理GCAU字母表上定义的景观比仅限于纯GC序列的景观要平滑得多，并且相关长度几乎是链长度的恒定分数。多结构景观的相关函数表现出增加的相关长度，特别是在解链温度附近。然而，对进化的主要影响相当于是有限种群采样的有效增加，其中每个序列探索多种结构。
