Origins of Enzyme Catalysis: Experimental Findings for C–H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs

• Published in: Journal of the American Chemical Society Vol. 139; no. 51; pp. 18409 - 18427
• Main Authors: Klinman, Judith P, Offenbacher, Adam R, Hu, Shenshen
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 27.12.2017
• Subjects: active sites; alcohol dehydrogenase; Alcohol Dehydrogenase - chemistry; Alcohol Dehydrogenase - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Biocatalysis; carbon-hydrogen bond activation; catalysts; catalytic activity; Catalytic Domain; geometry; Lipoxygenases - chemistry; Lipoxygenases - metabolism; Thermodynamics
• DOI: 10.1021/jacs.7b08418
• ISSN: 0002-7863; 1520-5126

The physical basis for enzymatic rate accelerations is a subject of great fundamental interest and of direct relevance to areas that include the de novo design of green catalysts and the pursuit of new drug regimens. Extensive investigations of C–H activating systems have provided considerable insight into the relationship between an enzyme’s overall structure and the catalytic chemistry at its active site. This Perspective highlights recent experimental data for two members of distinct, yet iconic C–H activation enzyme classes, lipoxygenases and prokaryotic alcohol dehydrogenases. The data necessitate a reformulation of the dominant textbook definition of biological catalysis. A multidimensional model emerges that incorporates a range of protein motions that can be parsed into a combination of global stochastic conformational thermal fluctuations and local donor–acceptor distance sampling. These motions are needed to achieve a high degree of precision with regard to internuclear distances, geometries, and charges within the active site. The available model also suggests a physical framework for understanding the empirical enthalpic barrier in enzyme-catalyzed processes. We conclude by addressing the often conflicting interface between computational and experimental chemists, emphasizing the need for computation to predict experimental results in advance of their measurement.