Free-Energy Maps of Base−Amino Acid Interactions for DNA−Protein Recognition
Free-Energy Maps of Base−Amino Acid Interactions for DNA−Protein Recognition
复制标题
DNA-蛋白质识别的碱基-氨基酸相互作用的自由能图
DOI：
--
复制
发表时间：
1999
期刊：
影响因子：
--
通讯作者：
A. Sarai
中科院分区：
文献类型：
--
作者：
F. Pichierri;M. Aida;M. Gromiha;A. Sarai
DNA-蛋白质识别在基因表达和调控中起着核心作用。尽管DNA-蛋白质复合物的结构数据越来越多，但DNA-蛋白质识别的分子机制还没有得到很好的理解，部分原因是碱基-氨基酸相互作用中相当大程度的冗余以及同一相互作用对中存在的结构灵活性。为了理解这种相互作用的特殊性，我们应该通过考虑结构灵活性来研究相互作用的能量学。我们描述了一种通过计算机模拟阐明DNA-蛋白质相互作用特异性的策略，其中氨基酸侧链和碱基对之间的相互作用的自由能通过广泛的构象采样来计算。模拟使我们能够估计热力学量，如相互作用自由能，焓，和熵，为每个给定的位置的Cα原子的氨基酸侧链的构象平均，并评估…
DNA−protein recognition plays a central role in gene expression and regulation. Despite increasing structural data on DNA−protein complexes, the molecular mechanism of DNA−protein recognition is not well understood yet, partly because of the considerable extent of redundancy in the base−amino acid interactions as well as of the structural flexibility present within the same interaction pair. To understand the specificity of such interactions, we should examine the interaction energetics by taking account of the structural flexibility. We describe a strategy for elucidating the specificity of DNA−protein interactions by computer simulation, in which free energies of interactions between the amino acid side chains and base pairs are computed by extensive conformational sampling. The simulations enable us to estimate thermodynamic quantities, such as the interaction free energy, enthalpy, and entropy, for each given position of the Cα atom of the amino acid side chain by conformational averaging, and to eval...