Sharma Pankaz K, Chu Zhen T, Olsson Mats H M, Warshel Arieh
Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9661-6. doi: 10.1073/pnas.0702238104. Epub 2007 May 21.
The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.
在某些方面,含辅酶B12辅因子的酶的催化能力一直是应变假说的“最后堡垒”。本研究通过采用克服了以往能量最小化研究采样困难的模拟方法,探索了这种效应的起源。研究发现,催化效应的主要部分是由于核糖与蛋白质之间的静电相互作用,而应变贡献非常小。值得注意的是,即使在自由基过程中,当反应片段的电荷分布在反应过程中没有显著变化时,酶也可以利用静电效应。在这种情况下,静电催化可以通过在离去片段上连接一个极性基团,并设计一个在产物状态下比反应物状态下与该基团相互作用更强的活性位点来实现。进化必须采用这种技巧这一发现,为非静电因素极难催化酶促反应这一观察结果提供了进一步的证据。事实上,B12酶所采用的这种技巧可能是酶设计中一种非常强大的新策略。