Enzymatic catalysis: the emerging role of conceptual density functional theory.
Experimentalists and quantum chemists are living in a different world. A wealth of theoretical enzymology-related publications is hardly known by experimentalists, and vice versa. Our aim is to bring both worlds together and to show the powerful possibilities of a multidisciplinary approach to study subtle details of complicated enzymatic processes to a broad readership. MD simulations and QM/MM approaches often focus on the calculation of reaction paths based on activation energies, which is a time-consuming task. A valuable alternative is the reactivity descriptors founded in conceptual DFT like softness, electrophilicity, and the Fukui function, which describe the kinetic aspects of a reaction in terms of the response to perturbations in N and/or upsilon(r), typical for a chemical reaction, of the reagents in the ground state. As such, the relative energies at the beginning of the reaction predict a sequence of activation energies only based on the properties of the reactants (Figure 5 ). In 2003, Geerlings et al. published a key review giving a detailed description of the principles and concepts of conceptual DFT and highlighting its success to study generalized acid/base reactions including addition, substitution, and elimination reactions. Since the time that this review appeared, conceptual DFT has proven its strength in literally hundreds of papers with application to organic and inorganic reactions. Its role in unravelling enzymatic reaction mechanisms, in handling experimentally difficult accessible biochemical problems, and in the interpretation of biochemical experimental observations is emerging and very promising.
Roos
Goedele
G
Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium. groos@vub.ac.be
Geerlings
Paul
P
Messens
Joris
J
D053502:Arsenate Reductases / Q000737:chemistry; D001665:Binding Sites; D055162:Biocatalysis; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry; D010728:Phosphoenolpyruvate / Q000378:metabolism; D011789:Quantum Theory; D013879:Thioredoxins / Q000737:chemistry
D004798:Enzymes; D056572:Histone Deacetylase Inhibitors; D013879:Thioredoxins; D010728:Phosphoenolpyruvate; D053502:Arsenate Reductases