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生物学中的双核铜位点耦合:基于实验校准的计算视角

Coupled Binuclear Copper Sites in Biology: An Experimentally-Calibrated Computational Perspective.

作者信息

Stańczak Agnieszka, Kipouros Ioannis, Eminger Petr, Dunietz Eleanor M, Solomon Edward I, Rulíšek Lubomír

机构信息

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.

Department of Chemistry, Stanford University, Stanford, California 94305, United States.

出版信息

Coord Chem Rev. 2025 Feb 15;525. doi: 10.1016/j.ccr.2024.216301. Epub 2024 Nov 23.

Abstract

The broad class of O-activating coupled-binuclear copper (CBC) metalloenzymes contain a unique [CuO] catalytic core. This core is responsible for catalyzing challenging biochemical transformations, particularly the regioselective monooxygenations/oxidations of substituted phenols. Despite almost four decades of intense experimental and theoretical research, the factors governing the diverse reactivity of CBC enzymes had remained only partially understood. In this review, we highlight the recent synergy between spectroscopy, kinetic experiments, and state-of-the-art computations (including hybrid quantum and molecular mechanical, QM/MM, and advanced wave function theory, WFT, methods) that provided a conclusive mechanistic picture of the initial stages of the hydroxylation of phenolic substrates catalyzed by the CBC enzyme tyrosinase (Ty). We emphasize the power of calibrated theoretical calculations, supported by experimental spectroscopic and kinetic data on intermediates, in providing definitive insight into the catalytic reaction coordinate. We provide a critical review of previous efforts towards elucidating structure-function correlations over the four CBC protein classes (hemocyanins, catechol oxidases, tyrosinases, -aminophenol oxygenases). We outline how a systematic mechanistic understanding across the different CBC enzyme classes could uncover their elusive structure-function correlations, opening new possibilities for utilizing the [CuO] catalytic core outside its native biological context for applications in materials and biocatalysis.

摘要

广泛的O-活化双核铜(CBC)金属酶类含有独特的[CuO]催化核心。该核心负责催化具有挑战性的生化转化反应,特别是取代酚的区域选择性单加氧/氧化反应。尽管经过了近四十年深入的实验和理论研究,但对于CBC酶多样反应性的调控因素仍只有部分了解。在本综述中,我们着重介绍了光谱学、动力学实验与最新计算方法(包括混合量子与分子力学方法、QM/MM,以及先进波函数理论、WFT方法)之间最近的协同作用,这些协同作用为CBC酶酪氨酸酶(Ty)催化的酚类底物羟基化初始阶段提供了确凿的机理图景。我们强调了经校准的理论计算的作用,其得到了关于中间体的实验光谱和动力学数据的支持,能为催化反应坐标提供明确的见解。我们对之前在阐明四类CBC蛋白(血蓝蛋白、儿茶酚氧化酶、酪氨酸酶、对氨基酚氧化酶)结构-功能相关性方面所做的努力进行了批判性综述。我们概述了如何通过对不同CBC酶类进行系统的机理理解来揭示其难以捉摸的结构-功能相关性,为在材料和生物催化领域将[CuO]催化核心应用于其天然生物环境之外开辟新的可能性。

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