Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA.
J Am Chem Soc. 2012 Feb 22;134(7):3367-76. doi: 10.1021/ja208047b. Epub 2011 Nov 14.
The zinc sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Zn(II) binding induces a quaternary structural switch from a "closed" conformation to a more "open" conformation, reducing the DNA binding affinity by 4 orders of magnitude. In this study, we use classical molecular dynamics and quantum mechanical/molecular mechanical molecular dynamics simulations to investigate the molecular basis for the large conformational motions and allosteric coupling free energy (~6 kcal/mol) associated with Zn(II) binding. Our simulations successfully capture the closed to open allosteric switching in DNA bound CzrA on Zn(II) binding. They reveal that zinc binding quenches global conformational sampling by CzrA, whereas DNA binding enhances the mobility of residues in the allosteric metal binding sites. These findings are in close agreement with experiments. We also identify networks of residues involved in correlated and anticorrelated motions that connect the metal binding and DNA binding sites. Our analysis of the essential dynamics shows metal ion binding to be the primary driving force for the quaternary structural change in CzrA. We also show that Zn(II) binding limits the conformational space sampled by CzrA and causes the electrostatic surface potential at the DNA binding interface to become less favorable toward DNA binding. Finally, our simulations provide strong support for a proposed hydrogen-bonding pathway that physically connects the metal binding residue, His97, to the DNA binding interface through the αR helix that is present only in the Zn(II)-bound state. Overall, our simulations provide molecular-level insights into the mechanism of allosteric regulation by CzrA and demonstrate the importance of protein motion in its biological activity.
锌感应转录阻遏物金黄色葡萄球菌 CzrA 是一个很好的模型系统，可以帮助我们了解金属传感器蛋白如何维持细胞内金属的稳态。Zn(II)的结合诱导四级结构从“关闭”构象到更“开放”构象的转变，使 DNA 结合亲和力降低 4 个数量级。在这项研究中，我们使用经典分子动力学和量子力学/分子力学分子动力学模拟来研究与 Zn(II)结合相关的大构象运动和变构偶联自由能（~6 kcal/mol）的分子基础。我们的模拟成功地捕捉到了 DNA 结合的 CzrA 在 Zn(II)结合时从“关闭”到“开放”的变构开关。结果表明，锌结合会抑制 CzrA 的全局构象采样，而 DNA 结合则增强了变构金属结合位点残基的迁移率。这些发现与实验结果非常吻合。我们还鉴定了与金属结合和 DNA 结合位点连接的相关和反相关运动的残基网络。我们对基本动态的分析表明，金属离子结合是 CzrA 四级结构变化的主要驱动力。我们还表明，Zn(II)结合限制了 CzrA 采样的构象空间，并导致 DNA 结合界面的静电表面势能对 DNA 结合变得不利。最后，我们的模拟为通过αR 螺旋将金属结合残基 His97 与 DNA 结合界面物理连接的氢键途径提供了有力支持，该螺旋仅存在于 Zn(II)结合状态。总体而言，我们的模拟为 CzrA 变构调节的机制提供了分子水平的见解，并证明了蛋白质运动在其生物学活性中的重要性。
