通过其内在无序的连接区对单链DNA结合(SSB)蛋白的凝聚特性进行选择性工程改造。
Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region.
作者信息
Ecsédi Péter, Érfalvy Dávid, Kovács Zoltán J, Katran Viktoria, Pálinkás János, Cervenak Miklós, Pancsa Rita, Harami Gábor M, Smeller László, Kovács Mihály
机构信息
ELTE-MTA "Momentum" Motor Enzymology Research Group, De partment of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary.
HUN-REN-ELTE Motor Pharmacology Research Group, D epartment of Biochemistry, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary.
出版信息
Nucleic Acids Res. 2025 Jun 6;53(11). doi: 10.1093/nar/gkaf481.
Single-stranded DNA binding (SSB) proteins are essential components of genome metabolism in both bacteria and eukaryotes. Recently demonstrated condensation propensities have placed SSB functions in a new context regarding the organization of nucleic acid-modifying complexes. In this work, we provide functional dissection of the condensation and partner binding properties of Escherichia coli (Ec) SSB via engineered modifications of its intrinsically disordered linker (IDL) region. We identify specific alterations in two glycine-rich regions as well as aromatic and/or positively charged residues of the IDL by which a broad-range, selective modification of condensation propensity and condensate thermal and chemical stability can be achieved, while leaving the single-stranded DNA and partner protein binding functions of SSB unchanged. AlphaFold 3-predicted structures of tetrameric wild-type and engineered EcSSB constructs identify multiple possible binding sites for the conserved C-terminal tip on the tetramer core of the IDL, establishing a link between condensation propensity and restrictions in IDL conformational dynamics. Besides defining the contributions of IDL-driven interactions to driving protein condensation, these results pave the way for the definition of in vivo roles of EcSSB condensation via genetic engineering and delineate ways for further development of liquid-liquid phase separation prediction algorithms.
单链DNA结合(SSB)蛋白是细菌和真核生物基因组代谢的重要组成部分。最近发现的凝聚倾向将SSB的功能置于核酸修饰复合物组织的新背景下。在这项工作中,我们通过对大肠杆菌(Ec)SSB的内在无序连接子(IDL)区域进行工程改造,对其凝聚和伴侣结合特性进行了功能剖析。我们确定了两个富含甘氨酸区域以及IDL的芳香族和/或带正电荷残基的特定改变,通过这些改变可以实现对凝聚倾向以及凝聚物热稳定性和化学稳定性的广泛、选择性修饰,同时保持SSB的单链DNA和伴侣蛋白结合功能不变。AlphaFold 3预测的四聚体野生型和工程化EcSSB构建体的结构确定了IDL四聚体核心上保守C末端尖端的多个可能结合位点,建立了凝聚倾向与IDL构象动力学限制之间的联系。除了确定IDL驱动的相互作用对驱动蛋白质凝聚的贡献外,这些结果还为通过基因工程定义EcSSB凝聚在体内的作用铺平了道路,并描绘了液-液相分离预测算法进一步发展的途径。