Galzitskaya O V
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
Fold Des. 1997;2(3):193-201. doi: 10.1016/S1359-0278(97)00026-6.
It has been shown that not only the primary sequence but also the geometry of the native conformation influences the kinetic and thermodynamic properties of a protein-like model. The purpose of this paper is to elucidate the geometrical factor, which affects the kinetic and thermodynamic properties of RNA-like heteropolymers, and physical reasons for this phenomenon.
It is shown that increasing the strength of long-range contacts can accelerate the finding of the native secondary structure for RNA-like heteropolymers. Decreasing the strength of long-range contacts results in deceleration of this process. The physical reason for this phenomenon is the increase in the average energy of non-native structures and, as a consequence, the increase (in absolute value) of the relative value of native energy from strengthening long-range contacts under constant energy of the native state. Statistical analysis of natural RNAs has shown that the mean stability of helices formed by the pairing of regions that are remote along the chain prevails over the mean stability of helices formed by regions that are close along the chain.
The kinetics simulations suggest that the folding of the RNA secondary structure depends on the structural factors of the native state. One of these factors accelerating large RNA folding is the existence of strong long-range helices in the native secondary structure.
研究表明，不仅蛋白质样模型的一级序列，其天然构象的几何形状也会影响其动力学和热力学性质。本文旨在阐明影响RNA样杂聚物动力学和热力学性质的几何因素以及该现象的物理原因。
研究表明，增加远程相互作用的强度可以加速RNA样杂聚物天然二级结构的寻找过程。降低远程相互作用的强度会导致这一过程减速。该现象的物理原因是非天然结构的平均能量增加，因此在天然状态能量恒定的情况下，由于加强远程相互作用，天然能量的相对值（绝对值）增加。对天然RNA的统计分析表明，由沿着链远程区域配对形成的螺旋的平均稳定性高于由沿着链相邻区域形成的螺旋的平均稳定性。
动力学模拟表明，RNA二级结构的折叠取决于天然状态的结构因素。加速大型RNA折叠的其中一个因素是天然二级结构中存在强远程螺旋。
