Positively-Charged Semi-Tunnel Is a Structural and Surface Characteristic of Polyphosphate-Binding Proteins: An In-Silico Study

Phosphate is essential for all major life processes, especially energy metabolism and signal transduction. A linear phosphate polymer, polyphosphate (polyP), linked by high-energy phosphoanhydride bonds, can interact with various proteins, playing important roles as an energy source and regulatory factor. However, polyP-binding structures are largely unknown. Here we proposed a putative polyP binding site, a positively-charged semi-tunnel (PCST), identified by surface electrostatics analyses in polyP kinases (PPKs) and many other polyP-related proteins. We found that the PCSTs in varied proteins were folded in different secondary structure compositions. Molecular docking calculations revealed a significant value for binding affinity to polyP in PCST-containing proteins. Utilizing the PCST identified in the β subunit of PPK3, we predicted the potential polyP-binding domain of PPK3. The discovery of this feature facilitates future searches for polyP-binding proteins and discovery of the mechanisms for polyP-binding activities. This should greatly enhance the understanding of the many physiological functions of protein-bound polyP and the involvement of polyP and polyP-binding proteins in various human diseases.磷酸盐是所有核心生命过程必不可少的物质，尤其在能量代谢与信号转导中发挥关键作用。由高能磷酸酐键连接的线性磷酸盐聚合物——多聚磷酸盐（polyphosphate, polyP），可与多种蛋白质相互作用，作为能量来源与调控因子发挥重要功能。然而，目前学界对polyP结合结构的认知仍十分有限。本研究通过表面静电分析，在多聚磷酸盐激酶（polyP kinases, PPKs）及诸多其他polyP相关蛋白中，鉴定出一种潜在的polyP结合位点——带正电半隧道结构（positively-charged semi-tunnel, PCST）。我们发现，不同蛋白质中的PCST具有各异的二级结构组成。分子对接计算结果表明，携带PCST的蛋白与polyP的结合亲和力具有显著统计学意义。本研究借助PPK3 β亚基中鉴定出的PCST，预测了PPK3潜在的polyP结合结构域。这一特征的发现，为后续polyP结合蛋白的筛选以及polyP结合活性机制的解析提供了重要助力。该研究成果将极大推动学界对蛋白质结合polyP的诸多生理功能的认知，以及对polyP与polyP结合蛋白参与各类人类疾病机制的理解。