The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer

Abstract

The role of promoting vibrations in enzymic reactions involving hydrogen tunnelling is contentious. While models incorporating such promoting vibrations have successfully reproduced and explained experimental observations, it has also been argued that such vibrations are not part of the catalytic effect. In this study, we have employed combined quantum mechanical/molecular mechanical methods with molecular dynamics and potential energy surface calculations to investigate how enzyme and substrate motion affects the energy barrier to proton transfer for the rate-limiting H-transfer step in aromatic amine dehydrogenase (AADH) with tryptamine as substrate. In particular, the conformation of the iminoquinone adduct induced by AADH was found to be essential for a promoting vibration identified previously-this lowers significantly the 'effective' potential energy barrier, that is the barrier which remains to be surmounted following collective, thermally equilibrated motion attaining a quantum degenerate state of reactants and products. When the substrate adopts a conformation similar to that in the free iminoquinone, this barrier was found to increase markedly. This is consistent with AADH facilitating the H-transfer event by holding the substrate in a conformation that induces a promoting vibration.

Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase

“…Two opposing and limiting theories of enzyme catalysis revolve around the nature of mechanical and electrostatic fluctuations in the enzyme active site. In one of the theories, fast (approximately picosecond) vibrations (protein breathing modes) and a network of coupled motions within the enzyme-substrate complex have been hypothesized to be linked to transition state formation and reduction of the barrier for chemical change (10,13,15,21). It has also been suggested that dynamic excursions of active site architecture on the picosecond timescale create variable electronic interactions between enzyme and reactants, which induce catalytic barrier crossing (7,8,10,17,19).…”

“…The origins of the enormous catalytic power of enzymes are still not well understood despite enormous effort (1)(2)(3)(4)(5)(6). In particular, the functional role of fast picosecond protein motions in catalysis and the dynamic nature of the transition state barrier crossing is a subject of ongoing and current debate (7)(8)(9)(10)(11)(12)(13). Theoretical studies have suggested that fast vibrations in enzymes might generate transition state conformations conducive to the chemical reaction (7,8,(14)(15)(16)(17)(18)(19)(20)(21), a familiar concept for reactions in ordinary solvents (22).…”

Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions

“…Some workers believe that motions of the protein promote tunnelling Antoniou and Schwartz, 2001;Mincer and Schwartz, 2003;Mincer and Schwartz, 2004;Johannissen et al, 2007;Johannissen et al, 2008;Pang et al, 2008), while others believe that the degree of tunnelling is similar in enzymes and their equivalent reference reactions, i.e. in solution, and hence the effect is not catalytic (Hwang et al, 1991;Hwang and Warshel, 1996;Olsson et al, 2004).…”

Driving Force Analysis of Proton Tunnelling Across a Reactivity Series for an Enzyme‐Substrate Complex

“…[8] The enzyme reaction cycle is completed by long-range electron transfer to the type 1 copper protein azurin following assembly of an AADH-azurin electron transfer complex. [9][10][11] Insight into the reaction cycle has come from detailed analysis of the crystal structures of reaction intermediates, [8,9,12] computational simulations of the reaction chemistry [8,13,14] and isotope analysis of the proton transfer step using fast reaction stopped-flow methods. [5,15,16] These studies have provided a detailed appreciation of the reaction chemistry, whilst emphasizing the importance of proton transfer by quantum tunnelling mechanisms (for example, with tryptamine substrate).…”