The local topological free energy of proteins
The local topological free energy of proteins
复制标题
DOI：
10.1016/j.jtbi.2021.110854
复制
发表时间：
2021-08-17
影响因子：
2
通讯作者：
Panagiotou, Eleni
中科院分区：
文献类型：
--
作者：
Baldwin, Quenisha;Panagiotou, Eleni
蛋白质折叠，即蛋白质获得其功能所必需的三维构象的过程，仍然是生物学中一个尚未解决的重要问题。我们理解上的一个主要差距是蛋白质的局部特性如何与其整体特性相关。在本文中，我们利用环绕数（Writhe）和扭转数（Torsion）引入了一种新的局部拓扑/几何自由能，它可与蛋白质主链上连续的4个氨基酸相关联。通过分析从蛋白质数据库（PDB）中筛选出的蛋白质数据集，我们的结果表明，高局部拓扑自由能构象与序列无关，并且可能参与蛋白质折叠的限速步骤。通过分析一组二态单结构域蛋白质，我们发现这些蛋白质的总局部拓扑自由能与普拉克斯科等人（2000年）所报道的实验观测到的折叠速率相关。（C）2021爱思唯尔有限公司。保留所有权利。
Protein folding, the process by which proteins attain a 3-dimensional conformation necessary for their function, remains an important unsolved problem in biology. A major gap in our understanding is how local properties of proteins relate to their global properties. In this manuscript, we use the Writhe and Torsion to introduce a new local topological/geometrical free energy that can be associated to 4 consecutive amino acids along the protein backbone. By analyzing a culled protein dataset from the PDB, our results show that high local topological free energy conformations are independent of sequence and may be involved in the rate limiting step in protein folding. By analyzing a set of 2-state single domain proteins, we find that the total local topological free energy of these proteins correlates with the experimentally observed folding rates reported in Plaxco et al. (2000). (C) 2021 Elsevier Ltd. All rights reserved.