School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia.
Acc Chem Res. 2010 May 18;43(5):642-51. doi: 10.1021/ar900260c.
Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.
酶以非凡的选择性加速化学反应，使生命本身成为可能。理解导致这种高效催化的因素在我们利用酶的巨大力量的努力中至关重要。在这方面，计算化学已成为实验化学和生物化学的重要辅助手段，因为它以系统和直接的方式提供了结构与功能之间关系的详细见解。在本述评中，我们强调了我们最近在研究依赖辅酶 B(12)（或腺苷钴胺素，AdoCbl）的酶催化的基于自由基的反应方面的高级理论研究。除了它们在生物学中的基本地位外，AdoCbl 依赖性酶代表了一个有价值的框架，可以理解自然界有效处理高能物质以执行非常特定反应的方法。AdoCbl 介导的反应的特征是在相邻碳原子上交换一个氢原子和一个官能团。我们的计算结果与以下结论一致，即 AdoCbl 的主要作用是提供自由基的来源，从而将 1,2-重排转移到自由基势能表面上。我们的研究还表明，部分质子转移涉及底物可促进自由基重排步骤。具体而言，我们观察到，通过适当的部分质子化或部分去质子化或有时（协同作用）两者，自由基重排的能量要求大大降低。这种相互作用与酶催化特别相关，因为酶活性位点中的局部氨基酸环境很可能通过氢键以这种方式发挥作用。最后，我们的计算表明，沿反应途径介入非常稳定的自由基可能会使酶失活，表明持续的催化依赖于微妙的能量平衡。基于自由基的酶反应通常难以通过实验进行探测，因此理论研究在其研究中具有特别有价值的作用。我们的研究表明，小模型方法可以为 AdoCbl 依赖性酶的作用机制提供重要而有启发性的见解。
