Combining experimental and theoretical methods to learn about the reactivity of gas-processing metalloenzymes

Claudio Greco (1) , Vincent Fourmond (2) , Carole Baffert (2) , Po-Hung Wang (3) , Sébastien Dementin (2) , Patrick Bertrand (2) , Maurizio Bruschi (4) , Jochen Blumberger (5) , Luca de Gioia (4) , Christophe Léger (2)

1 Department of Earth and Environmental Sciences [Milano]
2 IMM - Institut de Microbiologie de la Méditerranée
3 Institute of Oceanography [Taipei]
4 Dipartimento di Biotecnologie e Bioscienze
5 Department of Physics and Astronomy [UCL London]

After enzymes were first discovered in the late XIX century, and for the first seventy years of enzymology, kinetic experiments were the only source of information about enzyme mechanisms. Over the following fifty years, these studies were taken over by approaches that give information at the molecular level, such as crystallography, spectroscopy and theoretical chemistry (as emphasized by the Nobel Prize in Chemistry awarded last year to M. Karplus, M. Levitt and A. Warshel). In this review, we thoroughly discuss the interplay between the information obtained from theoretical and experimental methods, by focussing on enzymes that process small molecules such as H 2 or CO 2 (hydrogenases, CO-dehydrogenase and carbonic anhydrase), and that are therefore relevant in the context of energy and environment. We argue that combining theoretical chemistry (DFT, MD, QM/MM) and detailed investigations that make use of modern kinetic methods, such as protein film voltammetry, is an innovative way of learning about individual steps and/or complex reactions that are part of the catalytic cycles. We illustrate this with recent results from our labs and others, including studies of gas transport along substrate channels, long range proton transfer, and mechanisms of catalysis, inhibition or inactivation. Broader context Some reactions which are very important in the context of energy and environment, such as the conversion between CO and CO2 , or H+ and H2 , are catalyzed in living organisms by large and complex enzymes that use inorganic active sites to transform substrates, chains of redox centers to transfer electrons, ionizable amino acids to transfer protons, and networks of hydrophobic cavities to guide the diffusion of substrates and products within the protein. This highly sophisticated biological plumbing and wiring makes turnover frequencies of thousands of substrate molecules per second possible. Understanding the molecular details of catalysis is still a challenge. We explain in this review how a great deal of information can be obtained using an interdisciplinary approach that combines state-of-the art kinetics and computational chemistry. This differs from—and complements—the more traditional strategies that consist in trying to see the catalytic intermediates using methods that rely on the interaction between light and matter, such as X-ray diffraction and spectroscopic techniques.

Mots clés: electrochemistry; DFT; QMMM; theoretical chemistry; enzymes; bioinorganic chemistry

Domaines: Chimie inorganique; Chimie théorique et/ou physique; Biochimie, Biologie Moléculaire

Claudio Greco, Vincent Fourmond, Carole Baffert, Po-Hung Wang, Sébastien Dementin, et al.. Combining experimental and theoretical methods to learn about the reactivity of gas-processing metalloenzymes. Energy & Environmental Science, 2014, ⟨10.1039/c4ee01848f⟩. ⟨hal-01211585⟩