Yadav Shalini, Kalita Surajit, Dubey Kshatresh Dutta
Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University Delhi NCR, Gautam Buddha Nagar, Dadri, Uttar Pradesh, 201314, India.
Phys Chem Chem Phys. 2024 Nov 13;26(44):28124-28132. doi: 10.1039/d4cp03099k.
The recently discovered metal-free carbonic anhydrase (CA) enzyme may significantly impact the global carbon dioxide (CO) cycle, as it can irreversibly perform the CO hydration reaction. In this study, we investigated several key aspects of metal-free CA, including the identification of the catalytic site, the determination of the CO binding site, and the mechanism of catalysis. This is achieved through classical molecular dynamics (MD) simulations, quantum chemical density functional theory (DFT), and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our study indicates that the experimental structure based on X-ray crystallography, which shows the 'bicarbonate (HCO) product' trapped in the hydrophilic region of metal-free CA, might not accurately depict the actual enzyme-substrate interaction. Instead, the simulation reveals that CO prefers the hydrophobic zone, which serves as the primary catalytic site. It also highlights the strategic role of a gatekeeper residue (Phe504), which assists in regulating the transportation of CO by tilting its aromatic plane. Additionally, the hybrid QM/MM calculations establish that CO hydration is catalyzed within the hydrophobic zone by a deprotonated tyrosine with the help of an organized water chain.
最近发现的无金属碳酸酐酶（CA）可能会对全球二氧化碳（CO）循环产生重大影响，因为它可以不可逆地催化CO水合反应。在本研究中，我们研究了无金属CA的几个关键方面，包括催化位点的识别、CO结合位点的确定以及催化机制。这是通过经典分子动力学（MD）模拟、量子化学密度泛函理论（DFT）和混合量子力学/分子力学（QM/MM）计算来实现的。我们的研究表明，基于X射线晶体学的实验结构显示“碳酸氢盐（HCO）产物”被困在无金属CA的亲水区，可能无法准确描述实际的酶-底物相互作用。相反，模拟结果表明CO更喜欢疏水区域，该区域是主要的催化位点。它还突出了一个守门残基（Phe504）的关键作用，该残基通过倾斜其芳香平面来协助调节CO的运输。此外，混合QM/MM计算表明，在疏水区域内，去质子化的酪氨酸借助有序水链催化CO水合反应。
