Computational studies of enzymic hydrogen tunnelling
thesisposted on 15.12.2014, 10:35 by Linus Johannissen
The importance of proton tunnelling in the reaction catalysed by the heterotetrameric enzyme aromatic amine dehydrogenase (AADH) has been extensively studied both kinetically and computationally, and the availability of crystal structures for key reaction intermediates makes this an ideal system for studying the involvement of dynamics in catalysis. Multi-nanosecond molecular dynamics simulations revealed that the motions of the reacting groups are not correlated with motions within the enzyme, and that the overall motions of the donor and acceptor atoms are not focused towards each other. Nevertheless, certain key motions are required to achieve tunnelling, and these were identified from spectral density analysis as corresponding to a 165 cm-1 promoting vibration. This vibration is not part of a large network of vibrations, but is instead inherent within the substrate, as confirmed by high-level frequency calculations of the isolated substrate. Comparing hybrid simulations of the heterotetramer and an isolated monomer of AADH revealed that this vibration is crucial for reducing the tunnelling distance and the height of the barrier separating the reactant from product by moving the system up the potential energy surface. numerical modelling of the experimental rates revealed that the promoting vibration is compatible with the reaction kinetics and compatible with the tunnelling distance derived from a concomitant computational analysis, and that the presence or absence of such a vibration may not be easily identified experimentally. This represents the first example of a short-range oscillation acting as a promoting vibration, and opens the door to new experimental methods for studying enzymic tunnelling and potentially for exploiting enzymes in biocatalysis by selectively exciting specific vibrational modes.