Free‐Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase

Abstract

The rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase, which is proton abstraction from the native substrate methylamine, is investigated using accelerated QM/MM molecular dynamics simulations at room temperature. Generation of the multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace maps two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 Å, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms-the OD2 site-is slightly favored in methylamine dehydrogenase by approximately 2 kcal mol , both kinetically and thermodynamically. Mechanistic analyses reveal that the hydrogen bond between Thr122β and OD1 is always present in the transition state independently of the proton transfer channel. Population analysis confirms that the electronic charge gained upon oxidation of the substrate is delocalized within the ring systems of the tryptophan tryptophylquinone cofactor.

Settling the Long-Standing Debate on the Proton Storage Site of the Prototype Light-Driven Proton Pump Bacteriorhodopsin

“…Here, we employed the Lagrangian metadynamics technique ,− in the ab initio QM/MM molecular dynamics framework. Ab initio metadynamics sampling has been successfully used not only for simulating chemical or enzymatic reactions in aqueous environments ,− but in particular for elucidating the mechanistic details of long-range proton translocation along hydrogen-bonded water chains in different enzymes/membrane bilayers. ,,,, The proton release pathway in bR was investigated using ab initio QM/MM metadynamics simulations employing the CP2k suite of programs. , The side chain atoms of Arg82, Ser193, Glu194, Glu204 together with eight water molecules were treated based on electronic structure calculations and, thus, constitute the QM system as depicted in Figure b, which was sufficient to translocate the proton to the exit channel. Four more water molecules, being initially part of bulk water and thus represented via the nonreactive TIP3P force field, were at that stage added to the QM system in order to fully release the proton from the end of the water wire in the exit channel deep into the bulk solvent.…”

Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

“…We note that the method of hybrid QM/MM calculations has been used in many earlier works to study the mechanism and energetics of several different enzymatic reactions. ,− However, to the best of our knowledge, such a study of the mechanism and free energy landscape of the transimination reaction of the PLP-SHMT complex in the presence of serine considering the full structural details of the enzyme, PLP, substrate, and surrounding environment is presented here for the first time. Given that the transimination process is a required pre-step for exhibiting the enzymatic activity of a PLP-dependent enzyme like SHMT, it is indeed important to have an understanding of the free energetics and reaction pathways of this process at molecular level.…”

Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes

“…We apply these methods for calculating 20 reaction energies of reactions (Fig. 1) related to the following enzymes (amongst others): citrate synthase (Bennie et al, 2016;Mulholland, Lyne & Karplus, 2000;Van der Kamp, Perruccio & Mulholland, 2007a;Van der Kamp, Perruccio & Mulholland, 2007b;Van der Kamp, Perruccio & Mulholland, 2008) (reaction 1-10, 14-17), aromatic amine dehydrogenase (AADH) (Johannissen, Scrutton & Sutcliffe, 2008;Masgrau et al, 2007;Pang et al, 2010;Ranaghan et al, 2017;Roujeinikova et al, 2007;Zelleke & Marx, 2017) (reaction 11), methylamine dehydrogenase (MADH) (Faulder et al, 2001;Nunez et al, 2006;Ranaghan et al, 2007;Tresadern et al, 2003;Zelleke & Marx, 2017) (reaction 12), proton transfer in a typical protein salt-bridge (reaction 13), class A β-lactamases (Chudyk et al, 2014;Hermann et al, 2003;Hermann et al, 2005;Hermann et al, 2006;Hermann et al, 2009;Langan et al, 2018;Meroueh et al, 2005) (reaction 18), fatty acid amide hydrolase (FAAH) (Lodola et al, 2005;Lodola et al, 2008;Lodola et al, 2010;Lodola et al, 2011;Palermo et al, 2014;Tubert-Brohman, Acevedo & Jorgensen, 2006) (reaction 19) and lysozyme (Bowman, Grant & Mulholland, 2008) (reaction 20), where reaction 1-13 and reaction 14-20 are proton transfer reactions and non-proton transfer reactions, respectively. These reactions represent widely different chemistry, and important classes of enzyme reactions: many of these enzyme reactions are model systems for testing and development of QM/MM methods.…”