Multiscale Modelling of Lytic Polysaccharide Monooxygenases

Abstract

Lytic polysaccharide monooxygenase (LPMO) enzymes have attracted considerable attention owing to their ability to enhance polysaccharide depolymerization, making them interesting with respect to production of biofuel from cellulose. LPMOs are metalloenzymes that contain a mononuclear copper active site, capable of activating dioxygen. However, many details of this activation are unclear. Some aspects of the mechanism have previously been investigated from a computational angle. Yet, either these studies have employed only molecular mechanics (MM), which are inaccurate for metal active sites, or they have described only the active site with quantum mechanics (QM) and neglected the effect of the protein. Here, we employ hybrid QM and MM (QM/MM) methods to investigate the first steps of the LPMO mechanism, which is reduction of Cu II to Cu I and the formation of a Cu II –superoxide complex. In the latter complex, the superoxide can bind either in an equatorial or an axial position. For both steps, we obtain structures that are markedly different from previous suggestions, based on small QM-cluster calculations. Our calculations show that the equatorial isomer of the superoxide complex is over 60 kJ/mol more stable than the axial isomer because it is stabilized by interactions with a second-coordination-sphere glutamine residue, suggesting a possible role for this residue. The coordination of superoxide in this manner agrees with recent experimental suggestions.

Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass

“…Such a role of this glutamine residue is also supported by recent quantum mechanics/ molecular mechanics (QM/MM) studies (Fig. 1C) (68). Accordingly, recent neutron structures of NcAA9D from Neurospora crassa (also known as NcPMO-01050) indicate that His157 and Gln166 (equivalent to His164 and Gln173 shown in Fig.…”

“…2). Earlier QM/MM calculations, in the working frame of an O 2 reaction mechanism, also suggested that the [CuO ϩ ] intermediate would be the relevant catalytic species (68,75,76). Still, other mechanisms, such as a mechanism involving the formation of a H 2 O 2 -derived hydroxyl radical as oxidant, cannot be excluded (32,44).…”

Reactivity of O 2 versus H 2 O 2 with polysaccharide monooxygenases

“…This is consistent with the evolution of an enzyme that would control the reactivity of the oxidant and limit turnover-dependent inactivation Perhaps the low k cat /K m(O 2 ) values combined with the high K m(O 2 ) values serve as a protective kinetic feature of PMOs in an effort to minimize uncoupled turnover. In addition, the PMO second coordination sphere residues are positioned to stabilize a cupric superoxide species (23,36,37). While extensive experimental work continually points to a cupric superoxide species for HAA by Cu enzymes (12,28,38), computational work has favored Cu-oxyl-based mechanisms for PMOs (39,40).…”

Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars

“…In a recent report, Hedegard and Ryde computationally calculated the C1–H and C4–H bond dissociation energies as 101.1 and 103.8 kcal/mol, respectively. 265 …”