Exploring enzyme chemistry through molecular simulation with QM/MM

  • Jonathan David Colburn

Student thesis: Doctoral Thesis (PhD)


Chapter 1 contains a detailed overview of the relevant theoretical background, including quantum chemical methods through density-functional theory and empirical potentials, as well as quantum-mechanics/molecular-mechanics (QM/MM) embedding methods, continuum solvation models, and methods for thermochemical corrections.

Chapter 2 describes results from high-level QM/MM calculations on a selection of heme peroxidase enzymes involved in lignin degradation. I demonstrate that existing conceptual models for their activity (and pH dependence) do not stand up to scrutiny and require substantial re-evaluation. I identify in previous studies the misattribution of some results to spurious effects from a residual system charge, which I argue is entirely artificial.

This chapter also describes protracted efforts to identify protein sites in lignin peroxidase that are potential mutation hotspots. I conclude that simple geometry screening protocols do not work and demonstrate the critical importance of first-principles modelling. However, I am able to validate a proposed mutant (LiP:D183N) from an earlier study with an increased redox potential and suggest a framework for active site design based on a more general environment model inspired by the well-developed concept of electrostatic preorganisation in adjacent literature. I also briefly explore the chemical modification of heme as an engineering strategy, and report calculations on a novel variant of lignin peroxidase incorporating ring-fluorinated heme.

Chapter 3 reports on the complete QM/MM characterisation of intra-molecular ester bond formation in the bacterial adhesin SaTIE:ED1. While I am able to identify an appropriate reaction path, I show from computed activation barriers that this highly unusual cross-link is unlikely to form in the crystalline phase following the proposed mechanism. I briefly address the implications of this for our collaborators, discuss alternative mechanism proposals, and explore several methods for presenting potential energies over multiple minima.
Date of Award6 Jun 2021
Original languageEnglish
Awarding Institution
  • University of St Andrews
SupervisorMichael Buehl (Supervisor)

Access Status

  • Full text embargoed until
  • 18 May 2023

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