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Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes
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Section:Abstract
Oxyanion holes stabilize oxygen anions in transition states. Data have been gathered both from enzyme structures and from corresponding structures from the Cambridge Crystallographic Database. The two data sets show a striking contrast. The small molecule interactions in the Cambridge database optimize hydrogen bonding. The enzyme active sites do not. Analyzing the data with the help of DFT calculations on theozyme-like models, we conclude that enzymes have not optimized binding to the transition state structures in reaction pathways involving oxyanion holes, because the best binding arrangement for the anions also optimizes binding for the starting materials of the reactions. Instead, enzymes arrange the hydrogen bonds so that the oxyanions are stabilized reasonably, but suboptimally, in order to avoid overstabilization of the ground state.
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On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models
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Shina C. L. Kamerlin, Zhen T. Chu, and A. WarshelThe Journal of Organic Chemistry2010 75 (19), 6391-6401Oxyanion holes play a major role in catalyzing enzymatic reactions, yet the corresponding energetics is frequently misunderstood. The main problem may be associated with the nontrivial nature of the electrostatic preorganization effect, without following ...
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- Published In Issue March 19, 2010
- Article ASAPDecember 29, 2009
- Received: July 13, 2009
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