Simulating DNA at low resolution
Simulating DNA at low resolution
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DOI：
10.1016/s0959-440x(96)80082-0
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发表时间：
1996-04-01
影响因子：
6.8
通讯作者：
Olson, WK
中科院分区：
文献类型：
--
作者：
Olson, WK
在过去的一年里，我们已经看到了几种新的数学方法的发展，用于分析双螺旋DNA的结构，并将链的序列依赖性特征纳入长聚合物的计算机模拟中。在这方面特别感兴趣的是各种蛋白质与DNA结合引起的局部和全局结构变化，从碱基对水平的微妙弯曲、解扭和滑动运动到数千个残基长的链中超螺旋结构的明显组织。计算工作还包括在长链模拟中结合DNA的非线性特征和其他环境力的新方法，以及跟踪由此产生的多种构型的新方法。这些集体进步指出了一些方法，这些方法将很快将大型基因组中的碱基对序列与折叠的三维结构联系起来，这些结构基于自然的弯曲、扭曲和平移趋势，并对不同蛋白质结合产生的变形作出反应。
The past year has witnessed the development of several new mathematical approaches to analyzing the structure of double-helical DNA and to incorporating the sequence-dependent features of the chain in computer simulations of long polymers. Of special interest in this respect are the local and global structural changes induced by the binding of various proteins to DNA, ranging from subtle bending, untwisting and sliding motions at the base-pair level to the apparent organization of supercoiled structure in chains that are thousands of residues long. The computational effort has also included both new ways to incorporate the polyelectrolyte character of DNA and other environmental forces in simulations of long chains and new methods to keep track of the multitude of configurations so generated. The collective advances are pointing to ways that will soon connect the sequences of base pairs in large genomes to folded three-dimensional structures based on natural bending, twisting and translational tendencies and in response to deformations produced by the binding of different proteins.