Kinetics of nucleic acid–large ligand interactions: Multiplet‐closure approximations and matrix‐iteration techniques
Kinetics of nucleic acid–large ligand interactions: Multiplet‐closure approximations and matrix‐iteration techniques
复制标题
核酸-大配体相互作用的动力学：多重闭合近似和矩阵迭代技术
DOI：
10.1002/bip.1981.360200808
复制
发表时间：
1981
期刊：
影响因子：
2.9
通讯作者：
I. Epstein
中科院分区：
文献类型：
--
作者：
Christopher E. Dateo;I. Epstein
开发并评估了近似方法，用于处理覆盖多个连续位点的均匀一维晶格（代表核酸或其他线性生物聚合物）的结合配体的速率。该模型仅需要结合所需的晶格位点数量、晶格位点总数（可能无限）以及配体在晶格上合作和非合作缔合和解离的基本速率常数作为输入。所采用的计算方法是将三重态闭合近似从螺旋螺旋（单位点配体）问题扩展到大配体结合问题。我们发现，考虑 n + 2 个晶格位点簇（其中每个配体覆盖 n 个位点）给出了动力学的令人惊讶的准确描述。该近似是通过 Craig 和 Crothers 提出的矩阵迭代方法的扩展来实现的。有限晶格长度的影响以及处理配体沿晶格运动的能力都被纳入其中。当考虑所有对称性时，矩阵迭代计算所需的时间仅随配体长度n线性增加，并且远小于用作比较标准的蒙特卡洛方法的时间。
Approximate methods are developed and evaluated for treating the rate of binding ligands that cover several contiguous sites to a homogeneous one‐dimensional lattice, which represents a nucleic acid or other linear biopolymer. The model requires as input only the number of lattice sites necessary for binding, the total number (possibly infinite) of lattice sites, and elementary rate constants for the cooperative and noncooperative association and dissociation of the ligand on the lattice. The computational methods employed are an extension of the triplet closure approximation from the helix–coil (single‐site ligand) problem to the large ligand binding problem. It is found that consideration of clusters of n + 2 lattice sites, where each ligand covers n sites, gives a surprisingly accurate description of the kinetics. The approximation is implemented by an extension of the matrix‐iteration approach proposed by Craig and Crothers. The effects of the finite lattice length, as well as the capability to treat ligand motion along the lattice, are incorporated. When all symmetries are taken into consideration, the time required for the matrix iteration calculation rises only linearly with the ligand length n and is considerably less than that of the Monte Carlo method, which is used as a standard for comparison.