Multiscale Modelling of Lytic Polysaccharide Monooxygenases

TL;DR

This study uses hybrid QM/MM modeling to investigate the activation mechanism of Lytic Polysaccharide Monooxygenases, revealing new stable structures and the role of specific amino acids in the process.

Contribution

It provides the first detailed hybrid QM/MM analysis of LPMO activation steps, highlighting structural differences from previous models and the stabilizing role of a Gln residue.

Findings

Equatorial superoxide complex is over 60 kJ/mol more stable than axial

The Gln residue stabilizes the superoxide binding in the active site

Structures differ significantly from previous vacuum-based calculations

Abstract

Lytic polysaccharide monooxygenase (LPMO) enzymes have attracted considerable attention due to their ability to enhance polysaccharide depolymerization, making them interesting in respect to production of biofuel from cellulose. The LPMOs are metalloenzymes that contain a mononuclear copper active site that can active dioxygen. However, many details of this activation are unclear, and have previously been investigated from a computational angle. Yet, these studies have either 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 of Cu(II) to Cu(I) and 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 vacuum calculations. Our calculations show that the equatorial isomer of the superoxide complex is over 60 kJ/mol more stable than the axial isomer, being stabilized by interactions with a second-coordination-sphere Gln residue, showing a possible role for this residue. Coordination of superoxide in this manner is in agreement with recent experimental suggestions.