大肠杆菌单链DNA结合蛋白的内在无序C末端尾巴调节与单链DNA的协同结合。

Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.

作者信息

Kozlov Alexander G, Weiland Elizabeth, Mittal Anuradha, Waldman Vince, Antony Edwin, Fazio Nicole, Pappu Rohit V, Lohman Timothy M

机构信息

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.

Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.

出版信息

J Mol Biol. 2015 Feb 27;427(4):763-774. doi: 10.1016/j.jmb.2014.12.020. Epub 2015 Jan 3.

Abstract

The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding.

摘要

同四聚体的大肠杆菌单链DNA结合蛋白(SSB)在DNA复制、修复和重组过程中发挥着核心作用。大肠杆菌SSB能够通过使用全部四个亚基([(SSB)65模式])或仅两个亚基([(SSB)35结合模式])以多种结合模式与长单链DNA(ssDNA)结合,其结合模式偏好受盐浓度和SSB结合密度的调节。这些结合模式表现出非常不同的ssDNA结合特性,其中(SSB)35模式对ssDNA表现出高度协同结合。SSB四聚体还能结合一系列伴侣蛋白,并将它们招募到作用位点。这是通过与连接到ssDNA结合结构域的四个C末端尾巴内固有无序连接子(IDL)的最后9个氨基酸(酸性末端)相互作用来实现的。在这里,我们表明IDL的氨基酸组成和长度会影响SSB蛋白的ssDNA结合模式偏好。令人惊讶的是,IDL的数量、单个IDL的长度以及酸性末端共同促成了(SSB)35结合模式中的高度协同结合。流体动力学研究和原子模拟表明,大肠杆菌SSB的IDL倾向于形成一组球状构象,而恶性疟原虫SSB的IDL则形成一组更伸展的无规卷曲。更多的球状构象与协同结合相关。

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