Department of Chemistry, Multiscale Research Institute of Complex Systems and Institute of Biomedical Sciences, Fudan University, Shanghai 200438, China.
National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
J Chem Inf Model. 2021 Feb 22;61(2):891-900. doi: 10.1021/acs.jcim.0c01119. Epub 2021 Jan 14.
The d-glucose/d-galactose-binding protein (GGBP) from is a substrate-binding protein (SBP) associated with sugar transport and chemotaxis. It is also a calcium-binding protein, which makes it unique in the SBP family. However, the functional importance of Ca binding is not fully understood. Here, the calcium-dependent properties of GGBP were explored by all-atom molecular dynamics simulations and Markov state model (MSM) analysis as well as single-molecule Förster resonance energy transfer (smFRET) measurements. In agreement with previous experimental studies, we observed the structure stabilization effect of Ca binding on the C-terminal domain of GGBP, especially the Ca-binding site. Interestingly, the MSMs of calcium-depleted GGBP and calcium-bound GGBP (GGBP/Ca) demonstrate that Ca greatly stabilizes the open conformation, and smFRET measurements confirmed this result. Further analysis reveals that Ca binding disturbs the local hydrogen bonding interactions and the conformational dynamics of the hinge region, thereby weakening the long-range interdomain correlations to favor the open conformation. These results suggest an active regulatory role of Ca binding in GGBP, which finely tunes the conformational distribution. The work sheds new light on the study of calcium-binding proteins in prokaryotes.
来自 的 d-葡萄糖/d-半乳糖结合蛋白（GGBP）是一种与糖转运和趋化作用相关的底物结合蛋白（SBP）。它也是一种钙结合蛋白，这使其在 SBP 家族中独具特色。然而，钙结合的功能重要性尚未完全阐明。在这里，通过全原子分子动力学模拟和马尔可夫状态模型（MSM）分析以及单分子荧光共振能量转移（smFRET）测量，研究了 GGBP 的钙依赖性特性。与之前的实验研究一致，我们观察到钙结合对 GGBP C 末端结构域的结构稳定作用，尤其是钙结合位点。有趣的是，钙耗竭 GGBP 和钙结合 GGBP（GGBP/Ca）的 MSM 表明钙极大地稳定了开放构象，smFRET 测量结果证实了这一结果。进一步分析表明，钙结合会破坏铰链区域的局部氢键相互作用和构象动力学，从而削弱远程结构域间相关性，有利于开放构象。这些结果表明钙结合在 GGBP 中具有活跃的调节作用，精细地调节构象分布。这项工作为研究原核生物中的钙结合蛋白提供了新的视角。
